The coral reef indices of biological integrity was constituted based on the reef check monitoring data. Seventy six minimally disturbed sites and 72 maximallv disturbed sites in shallow water and 39 minimally disturbed sites and 37 maximally disturbed sites in deep water were classified based on the high-end and low-end percentages and ratios of hard coral, dead coral and fieshy algae. A total of 52 candidate metrics was identified and compiled, Eight and four metrics were finally selected to constitute the shallow and deep water coral reef indices respectively. The rating curve was applied for each metric to identify two lower a and upper b threshold values. A set of scores 1.3 and 5 was used to score and narrate individual metric values. Each metric value at a site presented a poor. moderated or good condition of reefs. The index was calculated by averaging all selected metric scores. The overall site classification efficiencies were of 65.97 and 66,13% for shallow and deep waters respectively. Importantly, the strong negative correlation between indices and dynamite fishing -0.286 (p<0.01) and number of yacht within 1 km -0.185 (p<0.05) in shallow water and with poison fishing -0.279(p<0.05) and coral damaged by other factors -0.283 (p<0.05) in deep water indicated that coral reef indices were sensitive responses to stressors and can be capable to use as the coral reef biological monitoring tool.