Yeast endophytes are considered rare and occupy a small population of almost 6% in the entire endophytic community. They outshine bacterial and fungal endophytes in quite few aspects. In this study, yeast endophytes were targeted for isolation from young and healthy leaves of Capsicum assamicum from Guwahati region, Assam. It was further characterized using 18s rRNA ITS sequencing and phylogenetic analysis. Cellulase and lipase secreting potential of the isolated yeast endophyte was done on PDA plates supplemented with carboxymethyl cellulose (CMC) and Tween 20 respectively. Results revealed the presence of a pink pigmented yeast species and molecular characterization identified it as Cystobasidium calyptogenae. Also it exhibited good potential ability of lipase and cellulase secretion by clear zone formation around the colonies. However, this study further requires enzyme quantification assays and also this yeast endophyte could be used in biodiesel production and industrial bioconversion of cellulose.