Hammerhead sharks are particularly vulnerable to fishing because of their slow growth rate and reproductive constraints. This type of sharks needs special attention due to its conservation status. This research was aimed to describe the relationships of the hammerhead sharks from West Aceh waters with the hammerhead sharks from other places. Samples of the shark were collected from Ujong Baroh Fish Port, West Aceh. The samples were analysed at the Laboratory of Department of Marine Science and Fisheries, Syiah Kuala University. The laboratory activity was started with extraction of DNA enhanced by Polymerase Chain Reaction method and visualized by an electrolytical. Analysis using BLAST showed that the first sample obtained 94%-95% cover query value and produced a 683 base pair length while the second sample obtained 98% per sample for a cover query value and produced a 658 base pair length. The average nucleotide values of the hammerhead shark were T=32.8, C=26.6, A=25.7 and G=14.9. The phylogenetic tree shows that the hammerhead sharks from the study area were more similar to the hammerhead sharks from Australia and Malaysia. Overall, based on the nucleotide composition, phylogenetic tree and genetic distance, the hammerhead sharks from the study area are unique compared to the populations from the other places.