Abstract: Moso bamboo（Phyllostachys edulis） is an important economic bamboo species in China and has produced many variant types during its long-term cultivation and evolution. To understand the genomic variation and the mechanisms of morphological diversification for these variant types, “8” shape bamboo（P.edulis ′Bicanna′）, thick-wall bamboo（P.edulis ′Pachyloen′） and two individuals of wild P. edulis were taken as research materials to perform the whole genome in this study. The results showed that the number of SNP, InDel and SV in ′Bicanna′ was lower than that in ′Pachyloen′, but the number of non-synonymous SNP and InDel causing frame shift mutation was higher than that in ′Pachyloen′. The density of SNP was the highest on chromosome 19 and the density of InDel was the highest on chromosome 9. The results of phylogenetic analysis indicated that ′Bicanna′ and ′Pachyloen′ were clustered as sisiter group, supporting the inference that ′Bicanna′ was mutated from ′Pachyloen′. The GO functional annotation analysis of variant genes revealed significant enrichment in several processes including ADP binding, carbohydrate binding and defense response in ′Bicanna′ and ′Pachyloen′. KEGG functional annotation analysis revealed that the variant genes of both were annotated to 185 and 172 metabolic pathways, respectively. Sesquiterpenoid and triterpenoid biosynthesis pathways was significantly enriched in ′Bicanna′ and ′Pachyloen′. In addition, ion channels pathway was significantly enriched in ′Bicanna′, and pathway such as glycosyltransferases and enzymes with EC numbers were significantly enriched in ′Pachyloen′. The variant genes in these significantly enriched pathways may have important roles in the functional traits and morphogenesis of pole in ′Bicanna′ and ′Pachyloen′. The results of this study could provide important theoretical basis for the development of molecular markers among moso bamboo populations and variant types, as well as for the study of morphological diversity mechanisms in bamboo plants.