Abstract: The genus Corchorus is one of the most important fibre crops, in order to improve this largely neglected crop, it is essential to understand the pattern of diversity in this important crop species. In this study, inter and intra genetic diversity analysis of 40 genotypes from C. olitorius and 40 genotypes from C. incisifolus was carried out using sixteen RAPD markers. The molecular study of the two species classified C. olitorius into two main clusters with five genotypes unresolved while there are three clusters with all the genotypes clearly separated in C. incisifolus. The results of both inter and intra genetic diversities revealed a higher level of allelic diversity in C. incisifolus than in C. olitorius. In the morphological study, higher mean and higher upper range values for all the five quantitative traits in C. incisifolus indicated its superiority over C. olitorius. However, both species show divergent attributes in four qualitative traits but similar in two characters. This could be attributed to higher level of natural outcrossing in C. incisifolus relative to that of C. olitorius. Results of this study therefore show that RAPD marker is a useful tool for assessing inter and intra genetic diversity in the two species of Corchorus. Therefore selection could be made from the diverse genotypes as parents for crosses designed for breeding improved jute cultivars and for producing mapping populations for QTL analysis.