Humpback whales were hunted to near extinction until whaling was banned in 1963. Population recovery is slow due to long generation times and human interference. Interestingly, it seems that the near decimation of humpbacks did not lead to a bottleneck effect on their genetic variety. We intend to assemble a haplotype genome (meeting CGP standards) of Cook Islands humpbacks to understand their genetic variation and compare inter-and intra-specific differences.