The concentration of metals in coral represents environmental changes, monsoonal variation, and human disturbance. Metals in coral were used as a proxy to evaluate the response of coastal areas to climatic and human stresses. In this study, several metals including lead (Pb), cadmium (Cd), chromium (Cr) and zinc (Zn) in Porites coral taken from Ambon Bay, Ambon Island, Indonesia, were investigated. The history of metals transient in the most populated island in Maluku Province is documented here from measurements of metals concentration from monthly-banded coral that grew in coastal seawater from 2001 to 2009. The concentration of heavy metals in coral samples was measured using Flame Atomic Adsorption Spectrophotometry (FAAS) method. The results showed metals bioaccumulation (average ± STD) were following decreasing order: Pb (0.96 ± 1.58 μg/g) > Cr (0.15 ± 0.34 μg/g)> Zn (0.11 ± 0.26 μg/g) > Cd (0.007 ± 0.016 μg/g). Moreover, all metals content in the coral showed a remarkable rose from 2001 to 2009 and showed relatively high concentrations during the southeast monsoon for Pb and Cd. Based on the statistical analysis, all metals in Ambon Bay coral were impacted by terrestrial input. In addition, Pb and Cd were also impacted by natural processes that may be associated with their biogeochemical cycle and monsoonal variation.