The objective of the study was to validate molecular markers linked to genomic regions controlling flowering time in a set of Recombinant Inbred Lines (RILs) population derived from Pusa 362 (Late) x BGD 132 (Early) and 21 diverse genotypes differing in time of flowering in chickpea (Cicer arietinum L.). The study of the polymorphic survey between parents using 27 linked markers of chickpea and Arabidopsis found 8 of them polymorphic. Bulked Segregant Analysis identified TA64 and TA142 as putatively linked to efl3 locus governing early flowering in chickpea that can be utilized for marker assisted selection. The PCR amplification of 6 polymorphic markers in germplasm showed the presence of one or more alleles in many of them (up to 3), indicating the complex nature of flowering time in chickpea. The amplification pattern of CaEfl3a-F1 marker linked to Efl3 early flowering allele of Arabidopsis in 21 chickpea germplasm indicated the presence of some conserved genomic sequences controlling flowering time in the two species.