Increased fish mortality due to infections has forced most farmers to resort the use of chemotherapeutic agents especially antibiotics. The continued use of these drugs in aquaculture is becoming limited as pathogens develop resistance and infer unpredicted long term public health effects. More research efforts are building to identify alternative disease prevention methods, among which the use of probiotics has been proposed. Therefore, the purpose of this study was to identify potential probiotics on surfaces of tilapia and catfish in areas around Kampala. Tilapia and catfish samples were aseptically collected from selected cages, ponds, tanks and hatcheries around Kampala, including Lake Victoria. The skin of fish was swabbed and then cultured on both general purpose and selective media. Probiotic screening was done using the agar spot method. Results revealed complete growth across all samples. The total microbial load was highest in fish from lakes (1000±9.6×10 5 cfu) and cages (1001±5.0×10 5 cfu). In all cases tilapia fish was significantly (p<0.0001) more contaminated than catfish. Out of the three strains of probiotics isolated, only Lactobacillus spp and Lactococcus spp showed antibacterial activity against pathogenic bacteria. The activity of Lactobacillus spp was significantly high (p< 0.0001) with Streptococcus spp (16.5±0.2 mm). Lactobacillus spp inhibited growth of only Proteus spp (5±0.2 mm). Our study shows that Lactobacillus spp and Lactococcus spp isolated from tilapia and catfish possess probiotic activity against a number of pathogenic bacteria. Our findings have significant implications for subsequent probiotic formulation and testing in aquaculture.