Species diversity indices provide quantitative data for understanding the variations and trends in fish species diversity, as well as information on species richness and evenness. However, these diversity indices do not reflect differences in specific taxa, which can be of importance as key conservation targets, especially during the planning and construction of protected areas. In this study, simultaneously combining our improved traditional fish fauna analysis (TFFA) with the value of fish fauna presence (VFFP) methods, we studied fish diversity in the Salween and Irrawaddy basins. The results of the TFFA reflected the families (subfamilies) and genera that constitute the main body of fish diversity in the river basins. The results of the VFFP assessment showed which families (subfamilies) and genera were representative of certain characteristics in the basins. The VFFP scores of genera could be used as indicator indices and as priority taxa in the planning and construction of fish resource reserves. In this paper, we propose for the first time that the role and status of monotypic genera (genera comprising only a single species) in the conservation of fish diversity should not be ignored, and they should rather be a priority for protection.