Increasing global seafood demand over the last couple of decades has resulted in overexploitation of certain fish species by both industrial and small-scale artisanal fishers. This phenomenon has threatened the livelihoods and food security of small-scale fishing communities especially in the West African sub-region. In Ghana, fish transshipment (locally referred to as saiko) has been catalogued as one more negative practice that is exacerbating an already dire situation. The goal of this study was to characterise transshipped fish species landed in Ghana on the basis of composition, habitat of origin, maturity and conservation status on the IUCN list of threatened species to enhance understanding of the ecological implications of the practice and inform regulatory enforcement and policy formulation. Using identification manuals, morphometric and gravimetric analyses among others, data on saiko fish samples landed at Elmina in the Central Region of Ghana were collected at bi-weekly intervals between November 2016 and June 2017. A total of sixty-eight (68) fish species from 44 families comprising finfish and shellfish of pelagic, demersal, benthopelagic, and reef-associated fishes were identified. The round scad (Decapterus punctatus), the mackerel scad (Caranx rhonchus), the round sardine (Sardinella aurita) and the red pandora (Pagellus bellottii) were the numerically dominant species recorded. By habitat classification, 44 species (65%) were demersals while 6 species (9%) were pelagic and 6 species (9%) were reef-associated. Majority of the demersal species were juveniles while composition of juveniles among the pelagic species ranged between 67% - 84%. In addition, 6 (10%) of the recorded species were either vulnerable or near threatened on the IUCN red list of threatened species. It could be deduced from these observations that the recruitment of juveniles into the small pelagic fish stocks may be compromised and possibly lead to the future collapse of such fishery. The practice is also inadvertently a clear threat to the marine ecosystem, and sustainable fish production in Ghana.