Fertility status and distribution of mating type alleles of Gibberella moniliformis and G. intermedia, both the causal agents of the foot rot and bakanae of rice, as well as stalk and root rot of corn were studied using specific primers. One hundred and twenty eight single-spore isolates were collected from rice growing areas of Guilan and Mazandaran and from various corn-growing areas of Iran. Sixteen isolates of G. moniliformis from rice and 54 isolates from corn, 28 isolates of G. intermedia from rice and 30 isolates from corn were taken into account for the study. Also 30 isolates of G. intermedia from corn and 12 isolates from rice, 5 isolates of G. moniliformis from rice were paired with standard tester isolates. A multiplex PCR technique was employed to distinguish idiomorphs MAT-1 and MAT-2 by using two pairs of specific primers GFmat1a, GFmat1b, and Gfmat2c, Gfmat2d. Among 68 isolates of G. moniliformis, 47 (69%) were identified as MAT-1 and 21 isolates (31%) belonged to MAT-2. Among 53 isolates 0f G. intermedia, 33 (62%) were identified as MAT-1 and 20 isolates (38%) belonged to MAT-2. Among 42 isolates of G. intermedia which were crossed with tester isolates, 26 (62%) were MAT-1 and 16 (38%) were MAT-2. The results of PCR were similar to those predicted as based on the results of crosses. Field isolates belonging to MAT-1 and MAT-2 were crossed with each other but no perithecium was formed. This indicated that all the isolates are female-sterile or male-fertile. The existence of both opposite mating type alleles with favorable frequency and different parents is an important occurrence of genetic diversity in the population of fungi. With regard to that, two mating type alleles found in the studied populations were of relatively high frequency of MAT-1 but because of the low level of female-fertile, occurrence of genetic diversity in the populations of G. moniliformis and G. intermedia coming from rice and corn could be attributed to other mechanisms of variability.