Highly polymorphic AFLP markers were applied to analyse the phylogenetic relationships of seven species from three sections within genus Araucaria (Araucariaceae) with cladistic and phenetic approaches. The objectives of the study were to compare the intrageneric relationships within Araucaria assessed by AFLP markers with the classification according to chloroplast DNA sequences and morphological characters. The AMOVA revealed 48% of the variation among species. The results of the principal coordinate analysis revealed three distinct groups: (1) A. angustifolia and A. araucana (= section Araucaria), (2) A. bidwillii (= section Bunya) and (3) A. cunninghamii, A. heterophylla, A. rulei and A. scopulorum (= section Eutacta). In the cladistic and phenetic analyses, phylogenetic trees were subdivided into two sister clades, one comprising the samples from section Eutacta, the other one was divided again into two sister clades corresponding to sections Araucaria and Bunya. These results are congruent with a previous phylogenetic study of the family Araucariaceae based on rbcL sequences and with the classification of genus Araucaria based on morphological characters. Both rbcL sequence data and AFLP analyses do not support section Bunya as one of the oldest sections within genus Araucaria, as suggested by the fossil record. The utility of AFLP markers for phylogenetic analyses is discussed.