Plant breeders are generally reluctant to cross elite cultivars with wild relatives to introgress novel desirable traits due to associated negative traits, such as pod shattering. This results in a bottleneck that could be dealt with better understanding of the genomic locations of the gene(s) controlling this trait. In this study, we integrated information on parental genomes, pod shattering data from multiple environments, and high-density genetic linkage maps to identify pod shattering QTLs in three lentil interspecific recombinant inbred line (RIL) populations. The findings from this study will be of significant value for lentil breeders to strategically access novel superior alleles while minimizing the impact of pod shattering from wild parents.