Reef degradation was investigated on 66 Egyptian Red Sea reefs—60 reefs for dynamite damage (using line transects) and six ship grounding sites (using 1 m sample squares). Ship groundings and dynamite fishing caused similar damage, reduction of the reef to rubble (65% of reefs were dynamited, mostly leeward, 58%). Changes in coral (line transect study) and fish communities (point count study) in impacted sites were documented. On impacted reefs, coral cover decreased, bare substratum and rubble increased, and fish dominance shifted away from Pomacentridae. Oceanographic conditions result in a stable pattern of coral communities (windward Acropora, leeward Porites). Most dynamite damage was on leeward, near-climax Porites reef slopes or Porites carpets. Most ship groundings were on windward Acropora reefs with regeneration periods calculated to be between 100 and 160 yrs. Regeneration time of dynamite damage is expected to be similar because of similar damage. Rehabilitation could speed up recovery but has to be consistent with natural community patterns. Coral transplants should mimic previously existing community structure in order to avoid space preemption by introduced superior competitors. Particularly if Acropora were introduced on a large scale into normally Porites dominated reef areas, re-establishment of the original community within the desired time-frame could be delayed.