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Background and Aim:  Baung fish is an essential commodity in Indonesia; however, few studies have explored the genetic diversity of Indonesian catfish. Thus, this study aimed to analyze the genetic variation and phylogenetic relationships among Indonesian catfish based on the mitochondrial  12S ribosomal RNA  ( rRNA ) gene.    Materials and Methods:  In total, 28 catfish were collected from nine rivers in seven provinces and from the Indian Ocean. Catfish genomes were obtained from epaxial and hepaxial muscle samples. The mitochondrial  12S rRNA  gene was amplified by polymerase chain reaction using a pair of primers (Baung12SF and Baung12SR). The  12S rRNA  sequences were analyzed using MEGA X to determine genetic variation and phylogenetic relationships.    Results:  In total, 178 variation sites in the  12S rRNA  gene were substituted among Indonesian catfish. The genetic distance between all Indonesian catfish samples was 0.1-16.0%. The closest genetic distance was between MP and PM catfish, whereas the farthest genetic distances were between BF and EM and PD and EM. For the entire population, based on mean diversity calculations, the number of base substitutions per site was 0.08.    Conclusion:  Indonesian catfish were divided into four clades based on the  12S rRNA  gene. The catfish MP, KR, PM, MS, BB, and KS were grouped with  Hemibagrus nemurus , the catfish EM was grouped with  Mystus vittatus , the catfish BSBJ was grouped with  Pangasius pangasius , and the catfish PD and BF were grouped with  Netuma thalassina .

Genetic variation and phylogenetic analysis of Indonesian indigenous catfish (baung fish) based on mitochondrial 12S rRNA gene