Classification and ordination methods used to examine the internal complexi
ty of the Mediterranean Tagus River catchment based on fish distribution re
vealed that it is not a homogeneous biogeographical unit. The indigenous fi
shes analyzed in this study are distributed through the basin forming geogr
aphical communities (chorotypes), some of which are associated with environ
mental factors like river morphology, water quality or geographical locatio
n. Nevertheless, 40% of the variation in species occurrence remains unexpla
ined by either environmental or geographical variables, suggesting that his
torical factors may influence the freshwater fish distribution patterns. Th
ree main biogeographical areas, delimited by significant boundaries, were i
dentified. Two of them are identified as the upper and the middle-lower bas
ins of the Tagus River catchment; the third corresponds to the Alagon River
and seems to be linked to historical factors of the catchment.