We report the thermotolerance of new bivoltine silkworm, Bombyx mori strains NB4D2, KSO1, NP2, CSR2 and CSR4 and differential expression of heat shock proteins at different instars. Different instars of silkworm larva were subjected to heat shock at 35℃,40℃ and 45℃ for 2 hours followed by 2 hours recovery. Heat shock proteins were analyzed by SDS-PAGE. The impact of heat shock on commercial traits of cocoons was analyzed by following different strategies in terms of acquired thermotolerance over control. Comparatively NP2 exhibited better survivability than other strains. Resistance to heat shock was increased as larval development proceeds in the order of first instar ＞ second instar ＞ third instar ＞ fourth instar ＞ fifth instar in all silkworm strains. Expression of heat shock proteins varies in different instars. 90 kDa in the first, second and third instars, 84 kDa in the fourth instar and 84, 62, 60, 47 and 33 kDa heat shock proteins in fifth instar was observed in response to heat shock. Relative influence of heat shock on commercial traits that correspond to different stages was significant in all strains. In NB4D2, cocoon and shell weight significantly increased to 17.52% and 19.44% over control respectively. Heat shock proteins as molecular markers for evaluation and evolution of thermotolerant silkworm strains for tropics was discussed.