Settlement and recruitment of the apogonids Apogon doederleini (Jordan & Snyder) and Cheilodipterus quinquelineatus (Cuvier) to continuous reef were examined at One Tree Island, southern Great Barrier Reef. Many settled to patch reefs in sand habitat. Moreover, peaks in settlement (over five to six days) corresponded to peak catches of potential settlers in ichthyoplankton nets at the reef crest. Few newly settled (<20 mm standard length) apogonids were found on continuous reef where juveniles and adults were abundant. A similar pattern was found on the reef slope outside the lagoon, but total abundance of both species was low in this environment. Results of tagging with tetracycline, diel censuses of patch reefs, and examination of gut contents indicated that fish of all size classes moved from daytime sites and foraged at night. Recruitment to continuous reef appears, particularly in A. doederleini, to take place in two phases: potential settlers enter the lagoon at night and settle into sand rubble habitats; fish feed at night and their night-time excursions increase with the size of the fish until they move to continuous reef as Phase 2. The monitoring of continuous reef would not have detected patterns of settlement to One Tree Island.