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Natives around the lakes historically dominated fishing on Lakes Victoria and Kyoga and the fishing gears consisted of locally made basket traps, hooks and seine nets made of papyrus. In view of changes in the fisheries of the two lakes, Frame surveys were conducted on lakes Victoria and Kyoga between 1990 to 2000. Selectivity characteristics of the fishing gears targeting the three major commercial fish species, the Nile perch, Nile tilapia and Mukene on the lakes were studied. Size at first maturity was determined for the three species in both lakes. Historical estimated annual fish catches, effort and catch per unit of effort (CPUE) data were analyzed for Lake Victoria Uganda (CPUE for entire lake) for period 1968 to 1998. Fish catches on Lake Victoria increased from 34,000 metric tones (t) in 1972 to 132,400 t in 1989 alongside an increase in fishing boats from 3000 to 8,000. However, a further increase in boats to 15,418 in 2000 resulted in the decline of the catches from 35 tonnes per boat per year to about 10 t. There was also increased use of longline, handline, beach seines, cast nets, traps, active fishing and mukene nets in different boat categories. Similar trends were observed on Lake Kyoga, where the CPUE had reduced to 14.6 t per boat per year in 1991. Usingvaluesofsizeatfirstmaturity,itwasobservedthattrawlcodends(inL.Victoria),passivegill nets and cast nets mesh sizes below 127mm cropped mostly immature Nile perch and Nile tilapia; boat/ beach seines also harvested mainly immature fish, but mukene nets of 5mm and above harvested mainly mature Mukene. Hooks of size 9 and bigger cropped over 75% mature Nile perch. Basket traps harvested immature Nile tilapia. In view of these trends, it is recommended that fishing effort be reduced to 8000 on Lake Victoria and to below 6500 boats on Lake Kyoga. Destructive fishing gears and practices should be prohibited. Passive fishing using a minimum mesh size of 127mm, drift netting only on Lake Victoria using a minimum gill net mesh size of 152.4 mm, hook fishing with minimum hook of size 9 and mukene nets not below 5mm mesh size operated offshore should be encouraged on both lakes. If trawling and cast nets are to be used (L. Victoria) they should be operated in waters deeper than 20m but the catches are very low and it is difficult to enforce the regulation. Trawling is already prohibited on Lake Victoria.