Epigenetic assays for estimating the age of humans have recently been developed based on age-induced changes in DNA methylation of specific genes. We used this information on age associated DNA methylation in human genes to identify homologous gene regions in humpback whales. In 2014, we successfully developed an epigenetic method for estimating humpback whale age with DNA from skin biopsy samples. Forty-five known-age humpback skin samples from a unique, intensively-studied population with individuals tracked since birth were employed to calibrate relationships between cytosine methylation and age. Methylation levels of 37 cytosines in regulatory regions of eight humpback whale genes were assayed and 7 were found to have a significant age-related profile. Three CpG sites with the strongest age-related methylation profiles were selected for the assay. This epigenetic age assay has an R2 of 0.82 and predicts age from skin samples with a standard deviation of 2.991 years. In 2015 we included another 27 known aged humpback whales to calibrate the assay. We found we had more variability and the R2 decreased to 0.73, however the age relationship remains significant. To demonstrate the potential of this technique, we constructed the first modern age profile of humpback whales off eastern Australia and compared the results to population structure 5 decades earlier. The modern age structure shows that there is still a deficit of older whales in this population that was hunted to near extinction in the early 1960s. Estimation of animal age by these sorts of non-lethal epigenetic biomarkers has great potential for enabling research on the population biology of many long-lived animals.