Vegetative compatibility groups (VCGs) were studied in 57 Fusarium oxysporum isolates from Momordica charantia L. (bitter gourd) and Lagenaria siceraria (Mol.) Standley (bottle gourd) using nitrate-non-utilizing (nit) mutants. Out of these, 24 isolates that sectored frequently in chlorate medium were genetically unstable and not further used in the experiment. Only 32 isolates were used, among them 21 from F. oxysporum f. sp. momordicae and 11 from F. oxysporum f. sp. lagenariae. Sixty one nit mutants were generated from 21 isolates F. oxysporum f. sp. momordicae with their respective frequencies: nit1 (31), nit3 (11), nit M (19). Twenty five nit mutants were generated from 11 isolates of F. oxysporum f. sp. lagenariae with their respective frequencies: nit1 (13), nit3 (5), nit M (7). F. oxysporum f. sp. momordicae populations have higher frequency of reversion to wild type (39.4%) than F. oxysporum f. sp. lagenariae (27.3%). Non-reverted mutants were used in complementation tests. Four VCGs of F. oxysporum f. sp. momordicae were identified with the majority belonging to a single VCG. Five VCGs of F. oxysporum f. sp. lagenariae were identified. Low VCG diversity ratio (VCGdiv = 0.19) was observed for F. oxysporum f. sp. momordicae whereas a higher value (VCGdiv = 0.45) was obtained for F. oxysporum f. sp. lagenariae. F. oxysporum f. sp. momordicae and F. oxysporum f. sp. lagenariae isolates were not vegetatively compatible.