The coral reefs structure and composition are influenced by environmental condition and depth. Therefore, this study was conducted to find and examine the influence of site and depth on coral reef structures in Pramuka Island regions, Seribu Islands, located in the northern of Jakarta. The study was carried out from November to December 2016. The data was taken by Line Intercept Transect Method which is laid 20 meters x 3 replicated parallels with shoreline at the depth of 3 and 10 meters. The hard coral at the depth of 3 m within both study sites in Pramuka island held higher percent cover than the depth of 10 m except in North of Pramuka. Coral mortality index varied and ranged from 0.39 to 0.98. West of Pramuka Island dominant hasthe lowest value of mean number of families, genera, and life form. Percentage of hard coral cover, coral mortality index, mean numberof family, genera, and life form differed significantly between sites. The different of depth only affecting the percentage of coral cover and mean number of life form. Corals have a limiting factor which are affected their development and growth.