Otolith shape analysis was used to identify 16 fish species belong to 5 families from the western Arabian Gulf to construct a cost-effective method of delineating fish taxonomic groups. We further tested the factors potentially affecting the identification process, including using different dataset sources, sex, the number of candidate species, different sample sizes and different sampling procedures. No specific dataset outperformed any other in the identification of fish families and species. Using all data sources yielded the best performance. Otolith shape parameters were significantly affected by somatic length, but not by sex. The correct prediction rate declined as the number of candidate species increased. An insufficient sample size led to a reduction in correct prediction rates with increased variability. The effects of size-biased sampling were species specific and could greatly reduce the correct prediction rate if the species of interest exhibits strong allometric changes in otolith shape. Having multiple sources of data, information a priori to reduce the number of candidate species and sufficiently large sample sizes across wide size classes so as to include possible variations in otolith shape are key to the precise identification of fish families and species using otolith shape analysis.