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Duyker was recruited by the Australian Department of Defence in Canberra in early 1981 and eventually worked in the Joint Intelligence Organization. He left in July 1983 to take up a position as a Teaching Fellow at Griffith University, Brisbane, but ultimately settled in Sydney as a full-time author in 1984.
Using the Dutch and French linguistic resources of his family, he edited The Discovery of Tasmania (1992) which brought together all known journal extracts from the first two European expeditions to Van Diemen's Land. An Officer of the Blue (1994), Duyker's biography of the explorer Marc-Joseph Marion Dufresne  was the subject of an essay, 'The Tortoise Wins Again!', by Professor Greg Dening, published in his collection Readings/Writings (Melbourne University Press, 1998, pp. 201-4).
François Péron: An Impetuous Life (2006), Duyker's biography of the zoologist of the expedition of Nicolas-Thomas Baudin to Australian waters (1800--1803), won the Frank Broeze Maritime History Prize in 2007.
In 2007 Edward Duyker published A Dictionary of Sea Quotations with a deeply personal introduction on his family's links with the sea.
Duyker's biographies of naturalists are largely conventional linear narratives, but they are characterised by meticulous research and great attention to detail - 'written with verve, but fortified with awesome scholarship' as Dymphna Clark put it in her review of Nature's Argonaut. He makes a point of visiting the places he writes about and orienting explorers' maps and journals to a modern landscape or coast.
Professor Thomas Nossiter of the London School of Economics praised Duyker's Tribal Guerrillas because 'it exemplifies the value of synthesising anthropology and history; and, more generally, it is a scholarly contribution to a literature on tribal rebellion and insurgency far wider than India, which embraces Greece, Vietnam and Algeria as well as sub-Saharan Africa where tribal responses to imperialism and modernisation have been significant' (Third World Quarterly, vol. 11, no. 2, April 1989, pp. 226-7). This meeting ground between history and anthropology can also be seen in An Officer of the Blue, Duyker's biography of Marc-Joseph Marion Dufresne, in which he skilfully used missionary and other accounts of M?ori oral history and French journals to explain the circumstances of the explorer's death in New Zealand's Bay of Islands in 1772. Prof. Barrie Macdonald of Massey University described it as "a fine piece of detective work - a biography written with an empathy with its subject yet a critical eye that helps set in context a death that still has its significance in New Zealand history."
Since 1985, Duyker has written more than 90 entries for the bilingual Dictionnaire de Biographie Mauricienne/Dictionary of Mauritian Biography published on his mother's native island. In November 2017, he was made an honorary member of the Société d'Histoire de l'Ile Maurice, in recognition of these contributions and for his books on the history of the Mauritians in Australia, Mauritian Heritage and Of the Star and the Key, Duyker has also written a number of pioneering monographs on the Dutch in Australia, and co-authored Molly and the Rajah (1991) * the life of Esme Mary Fink, an Australian woman who married the Rajah of Pudukottai, India, in 1915. He also edited A Woman on the Goldfields (1995),* dealing with the life of Emily Skinner on the nineteenth-century Victorian gold fields.
Duyker's writings span a diverse range of subjects and disciplines. In many respects he has built his readership on his eclectic interests and made a strength of them. The late Professor Greg Dening once described him as 'an historian's historian' (Australian Book Review, June/July 2003, p. 10).
Marius Damas, in his book (Approaching Naxalbari, Radical Impression, Calcutta, 1991, p. 68) commented that "Duyker brings both historical and anthropological tools into play . . . Drawing on a wide range of historical and contemporary sources, including personal interviews . . . [and] provides us with a richly detailed account."
Reviewing An Officer of the Blue Professor Michael Roe (historian) wrote: "In building his story, Duyker has to confront matters of war, politics, geography, navigation, anthropology - the list could continue. He does so with constant skill and authority."
In 1995 Paul Brunton described Duyker's (and Per Tingbrand's) Daniel Solander: Collected Correspondence (1995) as 'a major contribution to textual scholarship'.
In 2006, Prof. Arthur Lucas, former principal of King's College London, wrote that Citizen Labillardière was an 'exceptionally readable, richly textured work . . . The life Duyker recreates is as rich as that of the hero of any adventure novel, and the context is insightful history, not just the history of an important natural historian'.
Duyker's biography of French explorer Jules Sébastien César Dumont d'Urville was shortlisted and a runner-up for the 2015 Frank Broeze Maritime History Prize. One of the judges wrote that it was 'a thoroughly and meticulously prepared history of one of the giants of French voyaging'. Another judge described it as a 'monumental work'.
(With Maryse Duyker) Beyond the Dunes: A Dutch-Australian Story, Privately Published, Sylvania, 1987, pp. 41, ISBN0-7316-0058-4.
Of the Star and the Key: Mauritius, Mauritians and Australia, Australian Mauritian Research Group, Sylvania, 1988, pp. 129, ISBN0-9590883-4-2.
(With Coralie Younger) Molly and the Rajah: Race, Romance and the Raj, Australian Mauritian Press, Sylvania, 1991, pp. xii, 130, ISBN0-646-03679-3 [spoken word version: Hear a Book, Hobart, 2 track mono, 1993, abn 91 356351].
(ed.) The Discovery of Tasmania: Journal Extracts from the Expeditions of Abel Janszoon Tasman and Marc-Joseph Marion Dufresne 1642 & 1772, St David's Park Publishing/Tasmanian Government Printing Office, Hobart, 1992, pp. 106, ISBN0-7246-2241-1.
A French Trading Expedition to the Orient: The Voyage of the Montaran 1753--1756, Stockholm University Center for Pacific Asia Studies Working Paper, No.30, August 1992, pp. 20.
New Voices in the Southland: Multiculturalism, Ethno-history and Asian Studies in Australia, Stockholm University Center for Pacific Asia Studies Working Paper No.31, September 1992, pp. 15.
(with Hendrik Kolenberg et al.) The Second Landing: Dutch Migrant Artists in Australia, Erasmus Foundation, Melbourne, 1993, pp. 56, ISBN0-646-13593-7.
An Officer of the Blue: Marc-Joseph Marion Dufresne 1724--1772, South Sea Explorer, Miegunyah/Melbourne University Press, Melbourne, 1994, pp. 229, ISBN0-522-84565-7.
(with Barry York) Exclusions and Admissions: The Dutch in Australia 1902-1946, Studies in Australian Ethnic History, No. 7, Centre for Immigration and Multicultural Studies, Research School of Social Sciences, Australian National University, Canberra, 1994, pp. 11, ISBN07315 1913 2/ISSN 1039-3188.
(with Per Tingbrand, ed. & trans) Daniel Solander: Collected Correspondence 1753--1782, Miegunyah/Melbourne University Press, Melbourne, 1995, pp. 466, ISBN0-522-84636-X [Scandinavian University Press, Oslo, 1995 ISBN82-00-22454-6].
(ed.) A Woman on the Goldfields: Recollections of Emily Skinner 1854--1878, Melbourne University Press, Melbourne, 1995, pp. 129, ISBN0-522-84652-1. [RVIB, Melbourne, 2001, Spoken word version narrated by Ronnie Evans, one of 100 titles recorded by the Royal Victorian Institute for the Blind National Information Library Service in digital audio format for the 'Australians All project', funded by the National Council for the Centenary of Federation.]
Nature's Argonaut: Daniel Solander 1733--1782, Naturalist and Voyager with Cook and Banks, Miegunyah/Melbourne University Press, Melbourne, 1998 (reprinted 1999), pp. 380, ISBN0-522-84753-6 [Short-listed, New South Wales Premier's General History Prize, 1999]
[Introductory essay & biographical note] Mirror of the Australian Navigation by Jacob Le Maire: A Facsimile of the 'Spieghel der Australische Navigatie . . .' Being an Account of the Voyage of Jacob Le Maire and Willem Schouten 1615-1616 published in Amsterdam in 1622, Hordern House for the Australian National Maritime Museum, Sydney, 1999, pp. 202, ISBN1-875567-25-9.
(with Maryse Duyker, ed. & trans) Bruny d'Entrecasteaux: Voyage to Australia and the Pacific 1791--1793, Miegunyah/Melbourne University Press, Melbourne, 2001, pp. xliii, pp. 392, ISBN0-522-84932-6 [paperback edition, March 2006, ISBN0-522-85232-7].
Citizen Labillardière: A Naturalist's Life in Revolution and Exploration (1755--1834), Miegunyah/Melbourne University Press, Melbourne, 2003, ISBN0-522-85010-3, Paperback reprint, 2004, ISBN0-522-85160-6, pp. 383 (including notes, glossaries, zoological, botanical and general index), 12 maps, 18 black and white plates [Winner, New South Wales Premier's General History Prize, 2004].
'A French Garden in Tasmania: The Legacy of Félix Delahaye (1767--1829)', in Glynnis M. Cropp, Noel R. Watts, Roger D. J. Collins and K. R. Howe (eds.) Pacific Journeys: Essays in Honour of John Dunmore, Victoria University Press, Wellington, 2005, pp. 21-35.
'Isle de France and Baudin's Precursors in Australian Waters', in Rivière, M. S. & Issur, K. R. (ed.) Baudin-Flinders dans l'Océan Indien: Voyages, découvertes, rencontre: Travels, Discoveries, Encounter: Actes du colloque international organisé par l'Université de Maurice, octobre 2003, L'Harmattan, Paris, 2006, pp. 137-155.
François Péron: An Impetuous Life: Naturalist and Voyager, Miegunyah/MUP, Melb., 2006, pp. 349, ISBN978-0-522-85260-8 [winner Frank Broeze Maritime History Prize, 2007].
(ed. & compiler) A Dictionary of Sea Quotations: From Ancient Egypt to the Present, Miegunyah/Melbourne University Press, Melbourne, 2007, pp. 439, ISBN0-522-85371-4.
Marc-Joseph Marion Dufresne, un marin malouin à la découvertes des mers australes, traduction française de Maryse Duyker (avec l'assistance de Maurice Recq et l'auteur), Les Portes du Large, Rennes, 2010, pp. 352, ISBN978-2-914612-14-2.
Père Receveur: Franciscan, Scientist and Voyager with Lapérouse, Dharawal Publications, Engadine (NSW), 2011, pp. 41, ISBN978-0-9870727-0-2.
^Wallace Kirsop, 'Edward Duyker, or the Achievements of Independent Scholarship', Explorations (Institute for the Study of French-Australian Relations), no. 36, June 2004, pp. 17-18 & Greg Dening, 'Too Many Captain Cooks', Australian Book Review, June/July 2003, pp. 10-11.
^[National Library of Australia Oral History collection, ORAL TRC 3101 & TRC 5306 & Wallace Kirsop, 'Edward Duyker, or the Achievements of Independent Scholarship', Explorations (Institute for the Study of French-Australian Relations), no. 36, June 2004, pp. 17-18.]
^See Gunew, S., L. Houbein, A. Karakostas-Seda. & J. Mahyuddin (eds) (1992) A Bibliography of Australian Multicultural Writers, Deakin University Press (Centre for Studies in Literary Education), Geelong, 1992, pp. 71-2.