The present effort has been made to characterize the arecanut accessions based on total phenolic content and native protein profiles. The study showed significant variations for total phenolic content in the mature fruits among the arecanut accessions. Accessions VTL-26 (Fiji), VTL-11 (Indonesia) and VTL-60 (West Bengal) recorded higher phenolic content while low content was noticed in VTL-56 (Hirehalli Dwarf). The study indicated that protein profiles could be used for identification of individual accession of arecanut and cluster analysis also did not show any correlation between geographic affinity and genetic affinity of arecanut accessions in the cluster diagram.