Pigeonpea [Cajanus cajan (L.) Millspaugh] is one of the important tropical legume crops providing food and nutritional security largely to Asia and Africa. It is also known as tropical green pea, congopea, gungopea or no-eye pea. It is a diploid (2n=22), perennial woody shrub, often cross-pollinated crop belonging to the family Fabaceae. The pigeonpea genome was sequenced by two groups (Singh et al., 2011; Varshney et al., 2011), and its size was estimated to be between 833- 858Mb. Apart from being drought-tolerant, pigeonpea is also known to be heat-tolerant and grows well in the south Asian peninsula in the rainy season when the day temperatures are quite high. Under the current climatic regime which tends to be erratic, global warming will adversely impact almost all aspects of plant development, growth, reproduction and yield (Treshow, 1970). Organisms tend to maintain homeostasis during stress period (Boron, 2003). As compared to animals, plants are sessile organisms that cannot escape heat and are forced to adapt by modifying their metabolism to prevent damage caused by high temperatures. Various responses are exhibited by a plant during heat stress such as morphological damage, anatomical changes, physiological and expression of stress related proteins. These stress proteins are mainly responsible for the stability of other cellular proteins and membranes. During heat stress, protein denaturation starts and key regulators known as heat shock factors (Hsf), which regulate heat shock proteins (Hsp) are activated (Wu et al., 1995; Yamada et al., 2007; Fujimoto et al., 2010). The Hsfs recognize and bind to the conserved palindromic heat shock element (HSE- 5-AGAAnnTTCT-3) present in the promoters of most of the heat stress-inducible genes (Wu et al., 1995). The heat stress transcri