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Phytochemical and molecular characterization of Piper species was investigated. There was a wide variation of the active compounds present in leaf and fruits of different Piper species/accessions. Among the two active compounds, piperine-1 content was more in P. chaba fruit and Piperine-2 in P. nigrum fruit as compared with other species. Inter Simple Sequence Repeats (ISSR) marker was also used to analyze the genetic variation between the species/accession of Piper species. The phylogenetic analysis generated by ISSR marker was divided into two major groups with 47% similarity. First major group is only one species (i.e., Piper spp. Accession -1) and also morphologically distinct from other seven species. The second group is divided into two minor groups. Piper betle var. Godi Balunga and Piper betle var. Astarangi Balunga are grouped together with 100 % similarity at genetic level, whereas, Piper betle var. Utkal Sudhama having 97 % similarity with Piper betle var. Godi Balunga and Piper betle var. Astarangi Balunga. Both phytochemical and molecular marker showed significant variation among and between species/accessions. This study will help for the breeding program in Piper. [ABSTRACT FROM AUTHOR]