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It is often thought that Cunningham published few papers on botany and in his obituary, [[John Lindley]] wrote, "How little he regarded posthumous fame is seen by the fewness of his published works, a brief sketch of the Flora of New Zealand being the only systematic account of his Botanical discoveries...".<ref name="Lindl.">{{cite journal |last1=Lindley |first1=John |title=Miscellaneous Notices - Death of Mr. Allan Cunningham |journal=Edwards's Botanical Register |date=1840 |volume=26 |pages=1–3 |url=https://www.biodiversitylibrary.org/item/28967#page/295/mode/1up |access-date=24 April 2019 |archive-url=https://web.archive.org/web/20161110061741/http://www.biodiversitylibrary.org/item/28967#page/295/mode/1up |archive-date=10 November 2016 |url-status=live |df=dmy-all }}</ref> In fact, although he was effectively barred from publishing on botany whilst employed as "King's Collector", he nevertheless later published seven major papers, and 57 shorter papers on subjects including [[Taxonomy (biology)|taxonomy]], [[geology]], [[physical geography]] and [[zoology]]. He was one of the first scientists to publish papers on [[Phytogeography|botanical geography]].<ref name="Orchard2">{{cite journal |last1=Orchard |first1=Anthony E. |title=Allan Cunningham's cryptic publications |journal=Telopea |date=14 November 2013 |volume=15 |pages=191–204 |doi=10.7751/telopea2013022|doi-access=free }}</ref>
Cunningham was concerned that many of his discoveries sent to Kew were not published, allowing others, including [[William Baxter (botanist)|William Baxter]] to be credited with their discovery. (Baxter had risked arrest and a possible flogging for undermining Cunningham's work by sending specimens to commercial interests.)<ref name="Endersby">{{cite journal |last1=Endersby |first1=Jim |title=A Garden Enclosed: Botanical Barter in Sydney, 1818-39 |journal=The British Journal for the History of Science |date=2000 |volume=33 |issue=3 |pages=313–314|issn=0007-0874|jstor=4027955 |doi=10.1017/S0007087499004033 |s2cid=145561289 }}</ref> When Cunningham returned to London,
he sent duplicates of his herbarium specimens to other botanists, including [[Augustin Pyramus de Candolle|de Candolle]], [[Johannes Conrad Schauer|Schauer]], [[William Jackson Hooker]], [[George Bentham|Bentham]], [[John Lindley|Lindley]] and others, who published his descriptions with acknowledgement to "A.Cunn.".<ref name="Orchard" />
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