Background Many tilapia species or varieties have been widely introduced and have become an economically important food fish in China. Information on the genetic backgrounds of these populations is deficient and requires more research, especially for red tilapia strains. Methods In the present study, displacement loop (D-loop) sequences were used to evaluate the genetic relationship and diversity of seven tilapia populations that are widely cultured in China; this was done specifically to speculate on the maternal ancestry of red tilapia strains. Three red tilapia varieties of Oreochromis ssp. , Taiwan (TW), Israel (IL), and Malaysia (MY) strains and other populations, including O. aureus (AR), O. niloticus (NL), O. mossambicus (MS), and the GIFT strain of O. niloticus , were collected and analyzed in this study. Results A total of 146 polymorphic sites and 32 haplotypes of D-loop sequences were detected among 332 fish and four major haplotypes were shared among the populations. The TW and NL populations had a greater number of haplotypes (20 and 8, respectively). The haplotype diversity (Hd) and nucleotide diversity ( π ) of each population ranged from 0.234 to 0.826, and 0 to 0.060, respectively. The significant positive Tajima’s D value of neutral test were detected in the NL, IL, and MY populations ( P < 0.05), which indicated these populations might have not experienced historical expansion. According to the pairwise F -statistics, highly significant genetic differentiations were detected among populations ( P < 0.01), with the exception of the IL and MY populations ( P > 0.05). The nearest K2P genetic distance ( D = 0.014) was detected between the MS and TW populations, whereas, the farthest ( D = 0.101) was found between the GIFT and AR populations. The results from the molecular variance analysis (AMOVA) showed that there was an extremely significant genetic variation observed among the populations ( P < 0.01), which contained 63.57% of the total variation. In view of the genetic relationship of red tilapia strains with other populations, TW and IL were detected with more similar genetic structures related to MS, and MY was more genetically similar to GIFT (or NL), which could provide more genetic evidence for the red tilapia strains maternal ancestry.