The swamp eel () belongs to the family Synbranchidae, order Synbrachiformes. It is widely distributed in shallow lakes, rice fields, and swamps areas, especially in the Yangtze River region in China. It is one of the most important economic freshwater fishes because of its high meat quality, delicious taste, and medicinal value. Recently, it has been widely cultured in some regions, such as Hubei, Jiangxi, Anhui, and Hunan provinces. The production of in China in 2016 was 386,137,000 kg. However, most fries are sourced from fishing natural populations owing to a scarcity in fingerling resources from artificial reproduction. Therefore, with the challenges of overfishing and environmental deterioration, natural resources are sharply decreasing. It is vital to analyze the genetic background to conserve and utilize this fish effectively. The genetic diversity of six populations with 187 individuals from Hubei, Jiangxi, Anhui, Hunan, Chongqing, and Shandong was investigated based on the mitochondrial cytochrome oxidase I (COI) gene sequence. The results showed that the nucleotide composition of 646 bp in length was similar in the six populations. The average content of T, C, A, and G was 27.7%, 30.7%, 24.5%, and 17.1%, respectively. There were 61 mutation sites containing 16 singleton mutation and 45 parsimony informative sites. A total of 38 haplotypes were defined in all populations, and overall haplotype diversity () were 0.886 and 0.01094, respectively. In the six populations, the genetic diversity of Hubei and Shandong populations were the highest ( > 0.8), Hunan and Jiangxi populations were relatively high ( > 0.5), and Anhui and Chongqing populations were the lowest ( < 0.5). There was obvious genetic differentiation among six populations and gene flow was limited. An AMOVA analysis indicated that the source of variation within the populations was higher than between the populations. The major genetic variation was derived from variation within populations. A neighbor-joining phylogenetic tree showed that the genetic distance between the Hunan and other five populations was distant. The Chongqing population could originate from one single ancestor and a few populations. To date, the genetic diversity of natural populations is abundant. Furthermore, the genetic diversity did not sharply decrease, owing to the impact of the transaction and culture of M. albus to the environment and its breeding potential make this species a potentially excellent germplasm resource.