Flame retardants (FRs) are ubiquitously present in various environmental compartments due to widespread application. However, there have been few reports on the alternative FRs in harbor seals, and their relationship with fatty acid (FA) profiles have largely been overlooked. Here, we investigated the levels of legacy and alternative FRs and FA profiles in the blubber of harbor seals from the coasts of South Sweden (2009–2016) and Northeastern US (NE US) (1999–2010). We observed different proportions of mono- and poly-unsaturated FAs (MUFAs and PUFAs) between the two populations, which may reflect variations in the diet. Significantly higher concentrations of ΣPBDE were also observed in harbor seals from US compared to those from Sweden, both dominated by BDE 47. By comparison, the levels of alternative FRs, noticeably HBBZ and PBEB were much lower compared to those of PBDEs. Moreover, we found a positive correlation between BDE 99 and Σn-6/Σn-3 PUFA in harbor seals from Sweden. In addition, BDE 153 and BDE 154 were positively correlated with ΣUFA/ΣSFA in seals from Sweden and US, respectively. Our results imply the influence of diet in FA profiles and FR concentrations in top predators, as well as the importance of blubber FA characteristics in indicating FR exposure. Further investigations are required to assess the risk of exposure in these harbor seals, as well as to elucidate the underlying mechanisms associating FA profiles with FR exposure.