Lakes Victoria and Kyoga had many fish species, which were important as food for local population and valuable in scientific studies. Over the past twenty years, the diversity of fish in these lakes had declined due to over-exploitation, introduction of new fish species including the piscivorous Nile perch and degradation of fish habitat. This study examined fish species diversity in the seven small lakes in the Kyoga lake basin and compaired this with the main lake Kyoga (Iyingo) and historical data from Lake Victoria which have had high anthropogenic impacts. A total of 68 fish species were recorded of which 41 were haplochromines. Almost all the native non-cichlids which occurred in the main lakes (Victoria and Kyoga) before the Nile perch upsurge were recorded