Hervey Bay, Queensland is recognised as one of the only known stopover sites for the East Australian population of humpback whales. Historically, there is observational reports of individuals returning to the bay each season however, this study reports the first genetic evidence of kinship and matrilineal lines in this stopover site. SNP genotype sequencing was used to first examine the utility of SNPs with historic (2001, 2003, 2004, 2006) and contemporary (2022, 2023) sloughed skin samples (n = 182), then to understand relatedness and kinship within this population. We identified successful amplification of SNPs and historic tissues, with no significant change in DNA quality or quantity over time. Low-level relatedness was identified, with no variation in relatedness in the last two decades. Various kin relationships were detected within and between years, identifying successful detection of kin up to 21 years apart and matrilineal lines returning to the bay. The results contribute to our understanding of humpback whale population dynamics in migratory stopover sites and highlight SNP genotyping as an alternative to microsatellites and mitochondrial DNA that is favourable for degraded DNA, ideal for long-term studies and reproducible across laboratories and in turn, fostering a collaborative approach to marine mammal research.