Identification of fish bones from archaeological sites in southeast Arabia is challenging because of high taxonomic diversity, comparatively few reference collections with a wide range of species, as well as access to these resources. This paper provides illustrations of bones from many common taxonomic groups of fish from the southeast Arabia including several species of fish identified in very few assemblages, probably because of the lack of comparative reference material. This is a guide to aid other analysts in the identification process. We also consider the effect of reference collection size on the taxonomic diversity of analysed fish bone assemblages and conclude that research would benefit by the publication of further identification guides. Ideally these should include differences between closely related species, as this has a significant impact on the taxonomic diversity of archaeo-ichthyological assemblages. Although many papers are devoted to the influence of sample size, recovery method or recording protocols on the taxonomic diversity of faunal assemblages, a similar discussion on the effect of the reference collection used is often overlooked.