Fish stocks found on lagoon bottoms and near reefs are characterized by a high diversity and heterogeneous habitat which make stock estimation difficult. In particular, it is necessary to combine several methods in order to evaluate the major components of these stocks. The present study aimed at estimating reef fish stocks in the Northern Province of New Caledonia, a region where they represent a major target for the local fishermen. These estimates were based on experimental fishing with handlines and bottom longlines. Handlines were used to assess the stocks near reefs, and longlines for those in areas away from reefs and on lagoon soft bottoms. Handline stations (363) were sampled in three different regions (west, north and east lagoons) and three biotopes (nearshore, middle lagoon and barrier reef). A total of 104 species were caught, the major families being Lethrinidae, Lutjanidae and Serranidae. Species composition and catch per unit of effort (CPUE) varied among regions and biotopes. In particular, the north zone showed characteristics of an unexploited area with very high yields. An increase in CPUE and fish size from the coast towards the barrier reef and with increasing depth was observed in all regions. Correlations between CPUE from handlines and the numerical density and biomass estimates from underwater visual censuses (UVC) performed on nearby reefs were significant. A total of 206 longline stations were sampled in the west and east regions. A total of 80 species were caught, the major families being the same as those caught in stations with handlines with the addition of Carangidae. The CPUE of longlines was significantly correlated with numerical density and biomass estimates made by UVC along the longlines. Stock estimates based on the correlations between CPUE from handlines or longlines and UVC estimates indicate that 90 % of the lagoon stock were found on soft bottoms and near reefs. Reefs, despite biomasses that were five times larger than soft-bottom and near-reef areas, made only a small contribution to total stock. The ratio between density and CPUE was highest for the lowest densities, thus indicating that fishing efficiency increased with density. Comparison of handline catch performed around reefs and UVC data from nearby reefs suggests that there were bold relationships between the fish assemblages of these two biotopes.