With the development of MAB (marker-assisted breeding), pulse breeding has received another added tool in its armory for rapidly creating superior cultivars. Pulses, such as chickpeas, beans, and lentils, are an important source of protein for many diets dependent on their quantity and quality, making them a key component in sustainable agriculture and global food security. This chapter discusses the paramount role of molecular markers from biotic and abiotic stresses, yield enhancement, and nutritional quality. Developing key molecular markers such as SSRs, SNPs, and AFLPs has provided impetus to traditional breeding regimes for a faster selection process with fine-tuning of desirable traits such as disease resistance, drought tolerance, and nutritional enhancement. It has, for example, worked well in providing resistance to diseases such as Fusarium wilt in chickpeas and Ascochyta blight in lentils. Genome sequencing, QTL mapping, and recently developed genomic selection have shed light on our understanding of the genetic architecture of complex traits in pulses. However, with these gains, the application of MAB in pulses is still constrained by the scope and volume of existing genomics data and infrastructure, especially in areas where pulses are majorly grown. Nevertheless, these collaborations provide pulse breeders with enhanced measured genomic resources, and the rewards of future pulse breeding are likely to become apparent. Given the continuous evolution of genomic technologies, along with climate change and global food demand constraints, molecular markers and MAB will be pivotal tools in addressing the challenges that pulse crops face.