The use of medicinal plants to control reproduction in aquaculture have recently received considerable attention because they are biodegradable, safe, effective and locally available. However, information on their effects on gonadal characteristics and histological features in fish is currently limited. The present study evaluated the gonadal characteristics and histological changes of Nile tilapia, Oreochromis niloticus gonads fed on Aspilia plant, Aspilia mossambicensis and Neem tree, Azadirachta indica. Juvenile fish were fed diets supplemented with four doses (1.0, 2.0, 4.0 and 8.0 g/kg diet) of A. mossambicensis or A. indica leaf powders at 3% of their body weight daily for 90 days to examine absolute fecundity (AF), relative fecundity, gonadosomatic index (GSI) and histology of gonads. The antifertility phytocompounds in the two plants were quantified by using standard methods. Results indicated that, all doses of A. indica and A. mossambicensis used reduced significantly AF and GSI values (p < 0.05). Dose‐dependent histological alterations of gonads were noticed in both plants starting from doses of 2.0 g/kg in males and 4.0 g/kg in females. The highest percentages of total flavonoids (23.7%) and alkaloids (14.2%) were obtained from A. indica ethanol extract (p < 0.05). Taken together, dietary supplementation with A. mossambicensis and A. indica leaf powders alter gonadal characteristics of O. niloticus and histology triggered by alkaloids and flavonoids. Farmers interested in using the two plants to control prolific breeding should limit the dose inclusion to 2 g/kg to avoid severe effects on fish testis and ovaries.The United Republic of Tanzania through the Tanzania Commission for Science and Technology (COSTECH)