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BACKGROUD & OBJECTIVE: Piper, the pepper plants or pepper vines, are the genus of the Piperaceae family and areimportant economically and ecologically. It contains more than 1,000 species of shrubs, herbs and lianas, many of which arekeystone species in their native habitat. The diversification of this taxon is of interest to understand the evolution of plants. Inthe scope of bioactive compounds, Piper species (P. nigrum, P. retrofractum and P. longum) were screened forphytochemicals. METHODOLOGY: Phytochemical analysis of these plants showed presence of phenolic compounds,anthraquinones, terpenoids, flavinoids and lignin. Also, the methanolic extracts of these plants were tested for their antioxidantpotential by free radical scavenging activity by DPPH assay. All the tested plants showed antioxidant potential and the overallantioxidant activity of P. nigrum was found to be highest. Genomic DNA was extracted from the fresh leaves of selectedcultivars and PCR was performed by using RAPD primers to check the genetic diversity among these cultivars. From the PCRgenerated fingerprint, dendrogram was plotted by cluster analysis of similarity matrix. RESULTS: Dendrogram constructed bycluster analysis of RAPD markers showed that Piper nigrum and Piper retrofractum are closely related. Since morphologicaldifferences among these species are indistinctive, RAPD characterization can be helpful in their Discrimination.CONCLUSION: This finding can be used as prerequisite for plant breeding activities as well as for conservation of geneticresources.