The southeast Florida reef system faces a number of stress factors, among which ship groundings are one of the most physically damaging. Portions of the Florida reef tract located near Port Everglades, Broward County, Florida, USA have been damaged by ship groundings. In 2004, physical damage of more than 30,000 m2 was caused by the groundings of two large cargo ships, the MV Eastwind and MV Federal Pescadores. The present study was designed to measure differences of scleractinian coral recruitment patterns (recruit diversity and richness) and rates to these injured sites in comparison to undamaged reef sites. Coral recruitment rates were measured on unglazed ceramic tiles deployed for a period of one year from February 2007 to February 2008 at five different locations: three control sites (including a high coral cover site), and the two ship grounding sites. Morphology and genetic markers including CO1 and cytb were used to identify the coral recruits. A whole genome amplification kit (REPLI-g, Qiagen) was used to obtain sufficient amounts of DNA. Results revealed low recruitment rates (0.5-2.7 recruitsm-2 yr-1) to the studied sites, suggesting a low potential for recovery of the damaged areas.