The composition and structure of the larval fish community (LFC) in the NW Iberian upwelling system in late winter 2012 were examined, and the influence of abiotic and biotic factors on the horizontal distribution of fish larvae and on the horizontal structure of the LFC was investigated. The LFC, composed of 62 taxa (59 species and 3 genera) in 28 families, was dominated by Micromesistius poutassou followed by Scomber scombrus, Merluccius merluccius and Maurolicus muelleri. Multivariate analyses identified depth, sea surface temperature, geostrophic velocity and mesozooplankton biomass as the environmental factors involved in explaining variability in the LFC parameters (larval fish abundance, species richness and diversity) and revealed that the LFC was structured into coastal and slope larval fish assemblages. The main factor defining these assemblages was depth. However, the unusual coastal downwelling that occurred during the study would have participated in creating them and in maintaining assemblage boundaries, so that the importance of depth to the cross-shelf structuring of the LFC may have been overestimated. Our results suggest that larval fish assemblages in regions of coastal upwelling are driven by coastal downwelling during the winter mixing period and support the idea that fish larvae act as short-term (~10 d) biological tracers of the hydrography of the region during that period.