The two decisive enzymes in flavonoid biosynthetic pathway are chalcone synthase (CHS) and chalcone isomerase (CHI), wherein the former carries the first committed step of the pathway and later is involved in isomerization of chalcone. In the present study, full-length cDNA sequence of both the genes (PeCHS and PeCHI) from Phyllanthus emblica (L.) were cloned and sequenced. The 390 and 209 amino acid long polypeptides of PeCHS and PeCHI are coded by 1514 bp nucleotide (nt) (ORF 1173 bp) and 843 bp nt (ORF 630 bp) sequences respectively. Computational analysis revealed the deduced protein of PeCHS contained four CHS protein family specific conserved motifs including residues of active sites and other signature sequences. Four conserved amino acids Thr-48, Tyr-106, Asn-113, and Thr-190 at active sites were identified in PeCHI. Both PeCHI and PeCHS were expressed in E. coli BL21 using pQE-30 UA vector. Expression analysis was carried out in different developmental stages i.e. leaf, flower and fruits. Expression of PeCHS was maximum in mature fruit while PeCHI expression was highest in young leaves. With respect to fruit, PeCHI expression lower down first and then increases with the maturation of fruit whereas PeCHS expression increases gradually with the development of fruit.