Application of molecular markers in the establishment of germplasm characteristics is a common development in the recent years. Molecular markers have been applied in a wide range of crops like maize, rice among others, including cowpeas. With regards to cowpea studies that have been carried out in the recent years, systematic literature on molecular markers used in cowpea is limited. This literature review presents an overview on various aspects of molecular markers that have been applied in cowpea studies. Additionally, this review examines the various Molecular markers that have been used to study various aspects of cowpea such as diversity studies, development of genetic linkage maps and even quality trait loci mapping. This literature summary also presents the various challenges that are associated with the various molecular markers. According to the various studies used in the summary, it is evident that SSR markers are common among cowpea diversity studies when compared to the other molecular markers. While hybridized based Diversity Array Technology (DArT) and even SNPs have become widely used in the study of other crops, cowpea studies on genetic diversity have not ventured in these techniques. This review provides useful literature for researchers and breeders on molecular markers with respect to cowpea.