DNA based molecular marker technologies have been used extensively to study the genetic relationships and to develop markers for identification of cultivars/varieties in various crops. The present study is an attempt to assess the variability and relatedness among 49 varieties/accessions of black pepper (Piper nigrum L.) based on the data generated by both RAPD and AFLP analyses. The similarity matrix was subjected to cluster analysis and dendrogram generated using the software Ntsyspc 2.1. The dendrogram revealed an average similarity of 63 per cent among accessions. Two selections from the variety Karimunda, namely Sreekara and Subhakara, together formed a single cluster with almost 92 per cent similarity. The dissimilarity observed between the varieties Panniyur 1 and Panniyur 3 the progenies of the same parentage, Uthirankotta and Cheriyakanyakadan was only 18 per cent. Based on RAPD analysis 34 varieties were grouped into 5 clusters. Distinct clustering was not observed in AFLP analysis. The results obtained were correlated with the taxonomical interrelationships reported for these varieties. The overall study has thus helped in understanding the relationship among the local cultivars and released varieties.