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Background Pigeonpea has considerable extent of insect-aided natural out-crossing that impedes genetic purity of seeds. Pre-anthesis cleistogamy in pigeonpea promotes self-pollination which helps in maintaining genetic purity. The cleistogamous flowers are linked with shriveled seeds, an undesirable trait from variety adoption point of view, and breeding using genomics tools can help in overcoming this constraint. Therefore, in order to identify genomic regions governing these target traits, one recombinant inbred line (RIL) population was developed using contrasting parents (ICPL 99010 and ICP 5529) for flower shape and shriveled seeds. The RILs were phenotyped for two years and genotyped using the Axiom Cajanus SNP Array. Results Out of the 56,512 unique sequence variations on the array, the mapping population showed 8634 single nucleotide polymorphism (SNPs) segregating across the genome. These data facilitated generation of a high density genetic map covering 6818 SNPs in 974 cM with an average inter-marker distance of 0.1 cM, which is the lowest amongst all pigeonpea genetic maps reported. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified 5 QTLs associated with cleistogamous flower, 3 QTLs for shriveled seed and 1 QTL for seed size. The phenotypic variance explained by these QTLs ranged from 9.1 to 50.6%. A consistent QTL “qCl3.2” was identified for cleistogamous flower on CcLG03 covering a span of 42 kb in the pigeonpea genome. Epistatic QTLs were also identified for cleistogamous flower and shriveled seed traits. Conclusion Identified QTLs and genomic interactions for cleistogamous flower, shriveled seed and seed size will help in incorporating the required floral architecture in pigeonpea varieties/lines. Besides, it will also be useful in understanding the molecular mechanisms, and map-based gene cloning for the target traits.