The composition, abundance and distribution of reef fish were strongly influenced by the trends in salinity, temperature and mixing regimes of the water during the three oceanographic cruises conducted in the vicinity of the marine reserve networks of Dipolog Strait. Forty-seven families of reef fish larvae were identified. Carangidae, Labridae, Scaridae, Gobiidae and Apogonidae were the top five most abundant larvae comprising 64.7 % of the total number of reef fish larvae collected. Shifts in the dominance of the top five most abundant reef fish families occurred primarily between the northeast and southwest monsoons coinciding with the changes in the temperature profiles of the water column. Abundance of reef fish larvae showed variability across the three sampling periods due to the succession of the dominant species of reef fish larvae. Fluctuations in salinity brought about by the transition from Northeast to Southwest monsoon period could explain the variation. Density distribution of reef fish larvae significantly increased with the increasing depth of the mixed layer during northeast monsoon period. The downwelling off the coast of southern Negros in February and April cruises contributed to the high abundance of reef fish larvae in this part of the strait, while the uniform mixing of the water column in June 2010 at southwest monsoon resulted in the weakening of density gradient of reef fish larvae.The study demonstrated the variable responses of the reef fish larvae to the gradients of chlorophyll in the Dipolog Strait. A better understanding on the retention mechanism of reef fish larvae along the coast of southern Negros, where the main marine reserve networks exist, is provided by the present study.