To explore the molecular mechanism of saponin biosynthesis from Chenopodium quinoa, variety Chenopodium quinoa cv. Longli 1 was used as materials, and experiment was carried out by using RT-PCR technology to identify the key enzyme which involved in triterpenes saponin biosynthesis. Then the conserved domain, secondary structure of protein and phylogenetic tree were analyzed by using bioinformatics methods, and organ-specific expression patterns of genes in seed, root stem and leaf were detected by semi-quantitative RT-PCR. The expression pattern of target gene were also investigated during seed developing period. Full-length cDNAs of CqSS1, CqSS2 and CqbAS were cloned, and gene expression results showed that both CqSS1 and CqbAS were highly expressed in leaf and seed than in other tissues, and express pattern remained in same level in different seed developing stage. This study is the first comprehensive analysis of the expression patterns of pivotal genes for triterpene saponin biosynthesis in Chenopodium quinoa, and provides a basis to further elucidate the molecular mechanism for the biosynthesis of saponin.