Abstract
Mackerel is a small pelagic fish that has potential value and can be found throughout Indonesian waters. It is feared that high exploration activities will have an impact on the population. Sampling was carried out at the fish landing port and fish auction place (Bacan, Morotai and Ternate). The sample was photographed and the 3 cm swimming fin was taken. The sample is then stored in a tube that has been filled with 96% ethanol solution. The next stage is the process of extraction, amplification, electrophoresis and DNA sequencing. Phylogenetic reconstruction of comparison of primary data (Bacan, Morotai and Ternate) and secondary data (Indian) clarified to form two different populations (clades). Amova population pairwaise (Fst) showed the genetic flow of R. kanagurta population in the waters of the north Maluku Sea (Bacan, Morotai and Ternate). On the other hand, genetic distance shows that populations (Bacan, Morotai and Ternate) were closely related and have strong genetic connectivity.