Habitat classification systems are poorly developed for tropical rainforests, where extremely high plant species richness causes numerous methodological difficulties. We used an indicator species approach to classify primary rainforest vegetation for purposes of comparative wildlife habitat studies. We documented species composition of pteridophytes (ferns and fern allies) in 635 plots (2×100 m) along 8 transects within a continuous rainforest landscape in northeastern Peruvian Amazonia. Considerable floristic variation was found when the data were analyzed using multivariate methods. The obtained forest classification was interpreted with the help of indicator value analysis and known soil preferences of the pteridophyte species. The final classification included four forest types: 1) inundated forests, 2) terrace forests, 3) intermediate tierra firme forests and 4) Pebas Formation forests. This rapid and relatively simple vegetation classification technique offers a practical, quantitative method for large-scale vegetation inventory in complex rainforest landscapes.