In fish hatcheries, high densities of eggs are maintained in incubators with microbial loads that vary from those in the natural habitat. Moreover, the accumulation of organic debris on tools used in the hatchery facility assists the spread of infectious diseases. This study was designed to evaluate the effect of different iodophor concentrations (10, 50, 100 and 150 ppm) for different contact times (5, 10 and 15 min) on total bacterial count (TBC) and total fungal count (TFC) and hence on the hatchability percentage of tilapia eggs. In addition, the effect of common salt (NaCl), sunlight exposure, 1% Halamid®, 1% Virkon S® and 3% Aquazix® for contact times (5, 10 and 15 min) in reducing TBC and TFC on hatchery equipment (buckets, nets and dishes)was also evaluated. Iodophor treatment at 10 ppm for 15 min resulted in significant reduction of both TBC and TFC on tilapia eggs by ≥ 4 log10 reductions but failed to achieve complete disinfection of egg surface. Conversely, 50 ppm or higher iodophor concentrations did not display antimicrobial activity after all tested contact times. Hatchability percentage was insignificantly different between 0 ppm (90%) and 10 ppm (94%) of iodophor. However, 10 ppm iodophor was significantly different (P < 0.05) from 50 ppm (85%) and 100 ppm (65%). At 150 ppm, there was no hatchability. After application of different disinfectants, limited to general bactericidal activity of ≥ 4 log10 reduction was observed in common salt (NaCl 150 g /7 liters) after 15 min in dishes only, sunlight exposure after 10 min in dishes onlyand 3% Aquazix after 15 min in all tools. Significant and 100% log reduction of both TBC and TFC was observed in 1% Halamid®after 10 min and 1% VirkonS®after 15 min.