Temporal variability (seasonal and inter-annual) in the assembly of phytoplankton communities from the northern Alborán Sea was investigated. For this purpose, the taxonomic composition of the micro- and nano-phytoplankton communities at three fixed stations was determined every three months from 1994 to 2002. A total of 357 different taxa were identified. Most of them (about 54%) were diatom species belonging to 57 genera. Dinoflagellates and coccolitophorids accounted for 118 and 30 taxa respectively. Two time periods could be differentiated with respect to the cell abundance. Thus, the mean abundance from 1994 to 1999 was 338 cell ml-1 and it dropped to about 60 cell ml-1 during the period 2000-2002. Diatoms and un-identified small flagellates dominated the communities during this first period, although a significant increase in the abundance of coccolitophorids occurred after 1997. Pseudo-nitzschia, Leptocylindrus and Chaetoceros were the dominant genera. In contrast, the coccolitophorids Emiliania huxleyi and Gephyrocapsa spp. quantitatively dominated the communities from 2000 to 2002. These shifts in the community assembly were assessed by performing a sample-oriented stepwise discriminant analysis (SDA). The analysis separated the samples into three year-groups, with great inter-annual variability. In contrast, the SDA did not find any seasonal sucessional pattern. In spite of this result, chlorophyll a and cell abundance tended to be higher in the spring period, which has been described for the whole Alborán basin. The nutrient concentrations in the 75 m upper seawater layer had inter-annual fluctuations. Thus, NO3-+NO2-, PO4-3 and Si(OH)4 concentrations decreased significantly in 1997-1998. Additionally, lower Si(OH)4 concentrations and Si:P molar ratios were obtained in 2000. These results suggest that the inter-annual shifts in the phytoplankton taxonomic composition were due to alterations in the nutrient regime. In this paper we discuss the possible rationale for these nutrient changes.