Levels of 24 organochlorine compounds were investigated in wild mussels collected at two locations (Krka estuary and Kaštela Bay) on the Croatian Adriatic coast in 2003, 2005, 2006, 2007, and 2008. PCB and OCP ranges found at the two locations overlapped and followed similar profiles despite the differences between the two locations indicating that they share a common pollutants source. Among organochlorine pesticides, the dominant compound was DDT. Among indicator PCBs, the dominant compound was PCB-153, while PCB-118 was dominant among the remaining 11 congeners. Generally, the sum of six indicator PCBs was constantly greater than the sum of 11 congeners at both locations. α-HCH/γ-HCH and DDE/DDT ratios were below 1, indicating recent input of γ-HCH and DDT into the marine environment. In the investigated period, almost all organochlorine compounds reached the highest values in 2006. The levels of PCBs and OCPs in this study were considerably below the Croatian maximum permissible levels, confirming that they do not pose any threat for human health.