A genome-wide analysis of P450 genes was performed in waterflea genome based on their mRNA and amino acid data. Seventy-one P450 genes, assigned into 15 gene families and 17 subfamilies, were identified. They were partitioned into 12 groups and 16 orphan genes by a criterion that the genes belong to the same group when their amino acid identity was more than 60%. Except orphan genes and 4 gene groups, including 2 genes per group, positive selection and gene conversion were analyzed in other 8 groups, including 47 genes. The results showed that positive selection was detected in 3 groups (including 22 genes). The positively selected sites 228E or 277T, locating in SRS (substrate recognition sites) 2 or SRS 5, were detected in 2 groups (18 sequences) with a more than 95% probability, and gene conversions were detected in 5 groups (19 sequences). Interestingly, both positive selection and gene conversion events were identified obviously in 12 genes, and neither positive selection nor gene conversion event was detected in 18 genes. The correlation was revealed between positive selection and gene conversion: positive selection sites were identified in 63.2% of genes in which gene conversion events were detected, and gene conversion events were identified in 54.5% of genes in which positive selections were detected. Moreover, twenty motifs were identified, there in to, 5 motifs existed in over 90% of P450 genes.