This study was intended to studying polymorphisms of HSP70 and HSP90β genes and its possible association with heat resistance in Fayoumi and Leghorn chickens. Chickens of each breed were classified phenotypically to heat susceptible and heat resistant groups based on chicken behavior during heat stress period. PCR-RFLP technique was used to genotype HSP70 and HSP90β genes polymorphisms. Digestion of an amplified 360 bp of HSP70 gene with EaeI restriction enzyme resulted in three genotypes, E1E1, E1E2 and E2E2. Results analysis indicated that there were no significant differences of different genotypes between heat susceptible and heat resistant Fayoumi chickens. In Leghorn chickens the genotype E2E2 was found in almost heat susceptible chickens with frequency of 0.75% and can be used as a marker for heat susceptibility while, E1E1 genotype occurs with frequency of   0.6 % in heat resistant chickens and can be used as heat resistance marker. Digestion of HSP90β gene amplified 498 bp with MspI restriction enzyme resulted in one genotype M1M1 in both heat susceptible and heat resistant Fayoumi chickens. Also, all leghorn resistant chickens showed M1M1 genotype. While, the genotype frequency in Leghorn susceptible chickens were 0.7 M1M1 and 0.3 M1M2. Accordingly, the HSP90β heterozygous M1M2 genotype can be used as marker assisted selection for culling of heat susceptible birds.