Among abiotic stresses, heat stress has a large negative impact upon agricultural productivity worldwide. Moth bean (Vigna aconitifolia (Jacq.) Marechal) is attracting a great deal of attention due to its drought and heat stress tolerance nature although genotypic variability exists. Genotypes of moth bean were subjected to heat stress to reveal the pattern of expression of genes. Many heat shock proteins (HSPs) and Super oxide dismutase (MnSOD) are differentially regulated in plants subjected to heat stress. Twenty days-old moth bean seedlings were exposed to a temperature of 55°C for 30 minutes. Total RNA was extracted from stressed and control plants, proceed for qRT-PCR analysis. Heat shock protein (HSP70) and MnSOD were significantly up-regulated in Jwala, Jadia, Marumoth and RMO 40 genotypes of moth bean and downregulated in genotypes with accession numbers, IC 121051, IC 36392, IC 140725 and IC 472257. This study would help in identifying heat tolerant varieties in moth bean and related Vigna species for future breeding programmes.