He has mapped and analysed the distributions of all Indo-Pacific coral reef fishes.[6] Allen continues to publish scientific papers and is involved in the nonprofit organisation Conservation International, especially for the preservation of biodiversity in the area of Vogelkop Peninsula.
The rainbowfish Chilatherina alleni is "named in honour of Gerald R. Allen, in recognition of his outstanding contribution to ichthyology and his deep commitment to the study and preservation of the aquatic fauna of New Guinea." - Adrian R. Tappin
The little rainbow wrasse Dotalabrus alleni Russell 1988 was named in honor of Allen who collected the type series and drew Russell’s attention to the species that had not been previously described.[9]
The Wrasse Labropsis alleniRandall 1981 was named in honor of Allen who collected six of the fourteen type specimens.[10]
The sole Leptachirus alleniRandall 2007 is named after Allen who collected the type specimens.[11]
The skate Pavoraja alleni McEachran & Fechhelm, 1982 is named after him.[13]
The perchlet Plectranthias alleniRandall 1980 was named after Allen who provided the type specimens to Randall knowing that the species was undescribed and Randall would describe it.[14]
The goby Schismatogobius alleni Keith, Lord & Larson, 2017 in honor of Allen for his extensive work on the freshwater fish fauna of Papua New Guinea.[15]
The goby Stenogobius alleniWatson, 1991 is named in honor of Allen because of his contributions to the freshwater ichthyology of Papua New Guinea.[15]
^Christopher Scharpf & Kenneth J. Lazara (22 September 2018). "Order LABRIFORMES: Family LABRIDAE (a-h)". The ETYFish Project Fish Name Etymology Database. Christopher Scharpf and Kenneth J. Lazara. Retrieved 13 January 2022.
^Christopher Scharpf & Kenneth J. Lazara (22 September 2018). "Order LABRIFORMES: Family LABRIDAE (i-x)". The ETYFish Project Fish Name Etymology Database. Christopher Scharpf and Kenneth J. Lazara. Retrieved 13 January 2022.
^Christopher Scharpf & Kenneth J. Lazara (22 September 2018). "Order ANGUILLIFORMES: Family OPHICHTHIDAE". The ETYFish Project Fish Name Etymology Database. Christopher Scharpf and Kenneth J. Lazara. Retrieved 30 January 2022.
^Christopher Scharpf & Kenneth J. Lazara (22 September 2018). "Order RAJIFORMES (Skates)". The ETYFish Project Fish Name Etymology Database. Christopher Scharpf and Kenneth J. Lazara. Archived from the original on 26 December 2015. Retrieved 13 January 2022.
^ abcChristopher Scharpf & Kenneth J. Lazara (22 September 2018). "Order GOBIIFORMES: Family OXUDERCIDAE (p-z)". The ETYFish Project Fish Name Etymology Database. Christopher Scharpf and Kenneth J. Lazara. Retrieved 13 January 2022.