For the assessment of the benthic community health of Jinhae Bay using the Benthic Pollution Index, macrobenthic fauna samples were seasonally collected from 23 different sites between February, 2011 and November, 2012. The macrobenthic community health status was classified as “Poor” or “Very Poor” except for the bay mouth part of Jinhae Bay at the northern part of Geoje Island. A large proportion of functional Group IV and even azoic conditions appeared due to summer hypoxia at sites in sheltered regions of Jinhae Bay. Some of the dominant species recruited after summer hypoxia were Paraprionospio patiens, Sigambra bassi, and Theora fragilis belong to typical opportunistic species. By comparing the BPI values of the macrobenthic communities from other special management areas of Korea, Jinhae Bay was considered to have the lowest condition that was heavily polluted among special management areas.