Fusarium wilt [Fusarium oxysporum f. sp. melonis (Fom)],is one of the most serious diseases of muskmelon in India.Fifty accessions of muskmelon and its relatives collectedfrom diverse sources were subjected to molecular screeningwith Fom1 and Fom2 gene specific markers. Presence ofFom1 (R) gene was confirmed using RG-9-2 marker where assusceptible allele was confirmed with another set of primerS-TAG/GCC-470. Out of 50 germplasm lines, 16 lines werefound to be positive. Among which, eight were homozygousand eight were heterozygous in nature. The S-TAG/GCC-470 could only able to confirm susceptible allele in exoticlines but was failed to confirm the same in Indian accessions.While for Fom2 gene, a combination of R-408 (R allele) andS-342 (S allele) were used. Six genotypes containedhomozygous resistant gene while only three lines showedheterozygous nature for Fom2 gene. Only two genotypesviz., SM-2012-12 and IC-267359 contained both the resistantgenes, whereas Kajri Sel.1, IC-267375, MM-314 and MM-4305 contained Fom1 gene. These results conclude thepresence of novel resistant gene in Indian melon gene pooland there is an opportunity for developing new gene basedmarkers for these novel genes which will be useful tostrengthen the resistance against newly evolving pathogenicraces.