This study evaluated the impact of antimicrobial resistant bacteria produced by inland pollution sources on coastal areas, and investigates antimicrobial resistance profiles of bacteria isolated from marine filter feeders. A total of 107 shellfish (short-necked clams Ruditapes philippinarum, ark shells Scapharca broughtonii, and oysters Crassostrea gigas) were collected from the southern coast of Korea, from which 204 Escherichia coli strains were isolated. The antimicrobial susceptibility patterns of isolated strains were analyzed for 15 antimicrobial agents used in Korea for clinical or veterinary therapy. Antimicrobial resistance was present in 44.6% of E. coli isolates against at least one antimicrobial agent. The rate of antimicrobial resistance in the Narodo area was higher than isolates from the Gangjinman area and Kamak Bay. E. coli isolates had a higher rate of resistance against: tetracycline (29.9%), streptomycin (25.5%), and trimethoprim (14.2%). Of 204 isolates, 29 (14.2%) were resistant to multiple antimicrobial agents.