The wilt caused by Fusarium oxysporum f.sp. Ciceris is a major problem for chickpea. The large-scale discovery of DNA polymorphisms in different cultivars can provide insights into the genetic basis of phenotypic differences. In the present study, we sequenced the transcriptomes of four chickpea cultivars with contrasting response to Fusarium infection, including susceptible JG62 and resistant/tolerant ICCV2, K850 and WR315. Based on the analysis of their transcriptome sequences, we identified at least 303 polymorphic microsatellites, of which 64 % could be physically mapped on the chickpea genome. Further, we identified a total of 14,462 single nucleotide polymorphisms (SNPs) and 1864 insertions/deletions (InDels) among the chickpea cultivars analysed. More than 50 % of the SNPs and 19 % of the InDels were detected in the predicted coding regions, and about 46 % of these SNPs resulted in nonsynonymous changes. In addition, we identified at least 60 large-effect SNPs and 248 InDels that affected the integrity of the encoded protein. Several defence-related genes involved in different cellular processes were found to harbour nonsynonymous and/or large-effect SNPs and/or InDels. These data will provide functional markers and promising target genes for wilt resistance and present a valuable resource for molecular breeding for this important trait in chickpea. © 2015, Springer Science+Business Media Dordrecht.