Contributions of filamentous and picoplanktonic cyanobacteria to the phytoplankton community structure were examined in New Caledonian waters during the 2001-2003 El Niño period at 2 ocean stations (Loyalty Channel and Santal Bay) and 1 coral-reef lagoon station (Ouinne). Morphometric characteristics of diazotrophic filamentous cyanobacteria are given, as well as the seasonal and inter-annual variations of their surface areas and integrated abundances. Trichodesmium tenue and T. thiebautii were the dominant species followed by T. erythraeum, altogether accounting for more than 51-80% of the biomass of the free-living filamentous cyanobacteria. Katagnymene spp. accounted for a smaller percentage (<13.8% at ocean stations, <3.6% in the lagoon). Richelia intracellularis biomass was relatively small (<1% of total surface area and volume of Trichodesmium trichomes), with the highest concentration observed in summer (735 trichomes l-1). Colonies of unidentified cyanobacteria composed of spherical cells accounted on average for <1% of the Trichodesmium biomass, with maximum values exceeding 4000 cells l-1. Abundance of filamentous cyanobacteria varied according to environmental factors; summer 2001-2002 was characterized by low filamentous diazotroph abundance, and summer 2003, at the peak of the 2001-2003 El Niño, was particularly rich in filamentous cyanobacteria (with a maximum Trichodesmium spp. abundance of 4500 trichomes l-1 in the Loyalty Channel). A similar variability pattern was observed for large diatoms and dinoflagellates, and for all picoeukaryotic populations. Different biomass estimators are provided, including cell abundances, pigment concentrations including chlorophylls and phycoerythrin, and carbon content.