Abstract: In this study, different varieties of lotus ′Qingyu′ and ′Baiyangdianhonglian′ were selected as the research materials. The transcriptional sequence of petals at bud stage was sequenced by high-throughput sequencing technology. A total of 1 142 DEGs were identified from the 2 sample sequencing libraries, and the main genes of anthocyanin biosynthesis were screened out including ANS genes, CHS genes, DFR genes and UF3GT genes. Real-time PCR expression analysis showed that there was significant difference in the expression of 4 genes in the 2 kinds of flower petals at different stages. The highest expression level was at the bud stage or early flowering stage. This study lays the foundation for further study on the molecular mechanism of anthocyanin biosynthesis and flower color breeding.