The trnT-F region in chloroplasts was sequenced to elucidate interspecific phylogenetic relationships in the genus Cicer. Twenty-five species representing four sections and two outgroups were analyzed. A phylogenetic analysis revealed three major clades in the genus Cicer. Inferred phylogenetic relationships support multiple origins of annual species in the genus Cicer. Low variation within the most perennial species in the sequence regions suggests they may have originated during a period of rapid diversification after the genus arose. High levels of sequence divergence, biogeographical patterns and morphological traits between African and Eurasian groups of species suggest that Cicer may have independently diverged on each continent. Phylogenetic analysis of sequence data did not support the monophyly of the currently recognized sections and indicated the need for a revision of the infrageneric classification.