Wheat (Triticum aestivum L.) encounters 15–20% yield loss due to fungal diseases. A study was carried out to analyse the allelic variations in functional genes associated with multiple fungal disease resistance, viz. rusts, smuts and powdery mildew in 58 contrasting wheat genotypes. The experiments were conducted at Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana during 2020–21. A set of 29 simple sequence repeat (SSR) markers was selected for screening, out of which 24 markers showed amplifications (82.7%) and 23 showed polymorphism (95.83%) with a total of 46 alleles. Alleles per locus varied from 1 to 3 with a mean of 1.96 alleles per locus. At a similarity coefficient of 0.66, dendrogram grouped all the genotypes into 2 major clusters. Two and three dimensional plots also confirmed the distribution. Results showed that genotypes PBW 725 and WH 1268 were found to be most diverse at a similarity coefficient of 77%. SSR polymorphism rates were analysed using polymorphism information content, expected heterozygosity, marker index, discriminating power and resolving power values, where first two ranged from 0.03–0.65, and later three ranged from 0.03–1.94, 0.03–0.66 and 0.03–2.00, respectively. Based on these results, 8 proficient markers, viz. Barc232, Swm271, Xbarc124, Xbarc32, Xwmc44, Xgwm296, Gpw5029 and Xwmc557 are suggested for Indian wheat fungal disease resistance profiling. Among these, first two markers (Barc232 and Swm271) were detected in most (57) of the genotypes which are associated with ut6 and Lr75 genes, providing resistance to loose smut and leaf rust, respectively. This study can further help in gene pyramiding for producing multiple disease resistant genotypes.