Mercury (Hg) is a naturally occurring heavy metal, but human activities and natural processes have led to increased pollution with Hg in the environment. Organic mercury, such as methyl mercury (MeHg), is considered more toxic than most inorganic mercury compounds. MeHg is rapidly taken up by aquatic organisms and bioaccumulates through the aquatic food web. The bioaccumulation causes high levels of MeHg in apex predators, such as pilot whales. Pilot whale meat is a traditional food source on the Faroe Islands; thus the consumption of pilot whale meat can lead to high Hg exposures in humans. The majority of the total Hg in pilot whale and fish is generally assumed to be MeHg. However, the relative amount of MeHg to total Hg can be highly variable. For risk assessment, it is relevant to know both the MeHg and the total Hg content. This study summarizes the knowledge of muscle MeHg concentrations relative to total Hg concentrations in pilot whales in the Faroe Islands. The pilot whale tissue was sampled during 1977–78, 1986–87, 2009–2010, and 2015. The 2015 samples included two pairs of fetuses/mothers. The results showed that the 1977–78 pilot whale muscle samples had lower relative concentrations of MeHg to total Hg compared to samples from the subsequent years. This discrepancy between early and later years could not solely be explained by increased demethylation related to concentration differences. Instead, the difference is more likely explained by variations in relative amounts of MeHg in prey of the pilot whales. In the fetuses the total Hg concentration was 20% of the Hg concentration in the mother. The relative MeHg concentrations in the fetuses were also lower (∼20%–30%) than in the mother. However, the MeHg to total Hg fraction in the fetus was similar or higher than in the mother.