In order to study the genetic diversity and phylogenetic relationship of four wild-type or breeding populations (Oreochromis niloticus, O. aureus, O. mossambicus, GIFT Strain O.niloticus) and three red tilapia varieties (Chinese Taiwan, Israel, and Malaysia), sequences of mitochondrial cytochrome oxidase subunit I (COⅠ) were amplified by PCR and aligned. 180 polymorphic sites and 98 haplotypes were defined in 324 samples, with an average haplotype diversity of 0.944 and nucleotide diversity of 0.036. The negative Tajima's D values of neutral test were detected in GIFT, O. mossambicus and O. aureus populations, which indicated population size expansion after a bottleneck effect and/or purifying selection. The genetic distance of 7 tilapia populations was from 0.000 to 0.071, and the population genetic differentiation index (Fst) ranged from 0.016 to 0.994. Genetic population differentiation analysis (AMOVA) indicated that the majority of variation (70.78%) was attributed to variations among populations, whether grouping or ungrouping, reaching a very significant level. In this experiment, the purity of O. aureus was high, and the genetic diversity of the other six populations was rich. The population genetic structure of seven populations of tilapia was analyzed, which enriched the genetic background data of tilapia populations in China, and provided guidance for the utilization of tilapia germplasm resources, especially red tilapia.