Abstract The effect of two different nutrient input systems on Nile tilapia alone (Oreochromis niloticus), Blue tilapia (O.aureus) alone, as well as mixed of two species production was studied in eighteen earthen ponds. In the first system, chemical fertilizer (CF) 22.8 kg/feddan and 38.76 kg/feddan were applied weekly. In the second system, organic fertilizer at a rate of 420 kg/feddan/week, poultry manure for two months fol­lowed by artificial feeding 90 days using a diet containing 25% crude protein fed at a rate of 3% of fish biomass daily (OF) were applied in ponds. In each system sex reversed Nile tilapia alone (N) and blue tilapia alone (B), as well as, a mixed culture from both species (WI) at a rate of 1:1 were tested in three replicates each. Fish were stocked at a stocking rate of 8000 fish/feddan with an average weight 0.5gm on 1st July 1994. Duration of grow-out period averaged 158 days. Mean average fi­nal weight of Nile tilapia was significantly higher (106g) than blue tilapia (94g) and mixed culture of both species (95g) in chemical fertilization system and average yield was 582, 709 and 658 kg/feddan, respective­ly. In (OF) system, Nile tilapia had higher final weight (235g) and yield (1490 kg/feddan) than blue tilapia ((182g) and the mixed culture of both species (181g). Average final fish weight and yield within the same system differences were insignificant between (B) and (M). Physical, chemical and biological conditions were affected by fertilization system compared with fish species.