The distribution of planktonic organisms remains a central focus of research due to the fact that physical and biological interactions affect the marine pelagic ecosystem in different ways and at different scales. Therefore, different patterns in the structure of phytoplankton community emerge according to the observation scale. In the Chilean fjords systems, suggested to be autotrophic and showing neither a nitrate nor a phosphate deficit, we studied the phytoplankton structures from data sets obtained in four seasonal cruises across a large geographical region in Patagonia and Tierra del Fuego, including the biogeographic Magellan District and a portion of the Fuegian District (48-55 degrees S) separated in three sectors. We also processed a database from a spring cruise at a sub-regional spatial scale, which covers a portion of the central and southern Magellan sectors (52-55 degrees S) separated in seven areas with distinctive geographic characteristics. More defined patterns of microphytoplankton at large spatial scales were predicted, with greater heterogeneity and differences between assemblages at a smaller scale. Therefore, at a smaller scale particular local zones with characteristic phytoplankton assemblage are expected as a result of particular environmental conditions of the different geographical areas. In order to evaluate the phytoplankton community structure in both data bases, statistical tools such as multidimensional scaling (MDS), analysis of similarities (ANOSIM), Similarity Percentages (SIMPER) and Cluster Analysis were used when required. At a sub-regional mesoscale, principal component (PCA) and factor analysis were used for environmental data in order to determine if their distribution patterns influences the formation of local zones with similar microphytoplankton assemblages. A Canonical Correspondence Analysis (CCA) was performed to find the relationship between environmental variables and diatom and dinoflagellate grouped by genera. At the regional scale, clearly differentiated groups during the different seasons were found. Of these groups, the northern sector of the Magellan region (48-52 degrees S) forms a distinct group in all four seasons in agreement with a priori well known areas of higher probability of toxic shellfish detection, which have been defined as geographical Paralytic Shellfish Poison (PSP) toxicity cores, produced by a single toxic dinoflagellate species. These larger scale patterns respond to environmental forcing, probably temperature, winds, solar irradiance and circulation pattern. Results at a subregional scale showed no distinct microphytoplankton groups (Global R = 0.26), while significant differences between stations (p < 0.05) indicated a high heterogeneity within the same area. Temperature and nitrate were the most important variables correlated with the microphytoplankton genera groups. In conclusion, spatial regularities in microphytoplankton structure are found at the macroscopic scale (regional scale) and the PSP toxicity cores may be associated with changes in the composition and abundance of the entire microphytoplankton assemblage. Jointly, despite at small geographic scales, there is increased variability, several microphytoplankton local zones were detected and can be explained by exogenous influences, where nutrient input and temperature play the most important role. (C) 2014 Elsevier Ltd. All rights reserved.