Polygalacturonase (PG) synthetized by Fusarium spp. is a polymorphic enzyme with complex isoform patterns influenced by culture conditions and which are variable at the intra- and inter-specific levels. The partial sequence of an endopolygalacturonase coding gene (endopg) has been analyzed in isolates of seven species of Fusarium, most of them associated with Pinus pinea. The genomic fragment analyzed, 740 bp long, included two introns and the exon 4, which contained most of the amino acid motifs conserved in PGs from different origins. The high similarity of the amino acid sequences found among the isolates would indicate that differences in amino acid composition are not probably the main reason of the variability of this enzyme. Therefore, differences in the gene expression and regulation patterns of endopg gene among the isolates should be considered. Both types of sequences, the coding and the two intron sequences contained in the endopg fragment, were compared among the isolates to evaluate their potential use for phylogenetic studies. The different levels of variability of these sequences and the similar results obtained from the phylogenetic analyses when the three sequences (coding, intron and amino acid sequences) were used indicate that this endopg region would be very useful for phylogenetic analysis in the genus Fusarium.