A floristic inventory of woody plants was carried out to analyse the relationships between floristic similarity and geographical distance, and to compare the effect of land use history on the floristic composition between sites. Three lowland and two submontane sites were studied in Madidi, Bolivia. In one site, there is evidence of an Inca ruin. A total of 877 species and 12,822 individuals of woody plants with a diameter at breast height ≥2.5 cm were recorded in 44 0.1–ha plots. Fisher’s Alpha index values were slightly higher for the lowlands than for the submontane. Floristic similarity was higher within sites than between sites as measured by both Sørensen and Steinhaus indexes. The fact that the 30 most important species per site (totalling 94 species) accounted for 61.7% of total individuals, support the hypothesis that Amazonian plant communities are dominated by a limited set of species, genera and families. On the other hand, 18 out of the 94 species were reported in a single site, suggesting that some species are patchy in distribution and may be environmentally determined. Both the oligarchy and environmental-determinism hypotheses can be complementary in order to understand floristic patterns of this region. The Ruins submontane site is floristically the most distinct, and past human disturbance is likely to be the main reason. Since species diversity (ranging from 53 to 122 species per plot) and density (ranging from 157 to 503 per plot) are highly variable in Madidi, to characterize the diversity of a site, it is necessary to quantify an average of 10 0.1-ha plots in a relatively small geographical area.