Cowpea (Vigna unguiculata (L.) Walp.) is an ancient field crop that has been grown in Oman. Little is known about the morphological and molecular diversity of cowpea in Oman. The objective of this study was to characterize and evaluate Omani cowpea accessions morphologically and geneticall. A total of 25 accessions with 9 replication of each accessions were obtained from six different regions of Oman. At the morphological level, 17 qualitative and 6 quantitative characters showed variation among Omani cowpea accession and most traits were polymorphic. The standardized Shannon-Weaver diversity index (H) showed a mean (0.65) for quantitative characters higher than for qualitative characters (0.55). Overall, the morphological cluster analysis based on Ward's phenotypic diversity showed there was low genetic diversity with phenotypic distance of 180 within and between accessions obtained from different regions of Oman. AFLP analysis of 25 cowpea accessions with three replication from Oman and five commercial varieties of cowpea from neighbouring countries using 6 primer pair combinations produced 3057 polymorphic loci (99%). Moderate levels of genetic diversity (0.214 - 0.316) were found among populations of cowpea accessions obtained from different regions, despite the long history of cowpea cultivation in Oman. AMOVA analysis indicated the low level of genetic differentiation (FST = 0.032) among populations of Omani cowpea accessions, which suggests the informal exchange manner of seeds between farmers is common in Oman. In addition, AMOVA analysis showed that only 3% of the genetic variation exists among populations of cowpea, which suggests a high level of gene flow (Nm = 7.56) of cowpea accessions across geographical regions of Oman. Both analyses showed the Dhofar accessions were grouped in one subgroup and other accessions were intermixed in other subgroups. Overall, this study confirmed both markers (morphological and molecular) used gave similar results, showing low amount of phenotypic diversity in Omani cowpea accessions. The AFLP analysis showed low level of genetic variation. The study also confirmed that AFLP markers can be used for accessions analysis and reliable diversity evaluation.. This study clarifies the relationship between accessions of cowpea obtained from different 6 regions in Oman.