homeobox genes encode transcriptional factors, usually involved in molecular control of plant developmental patterns. they can be divided into several classes according to conserved sequences within the homeobox region and the presence of specific additional sequences. based on these conserved sequences, we developed a search procedure to identify possible homeobox genes in the eucalyptus genome sequencing project consortium (forests) database. we were able to identify 50 eucalyptus sequences (est-contigs) containing the homeodomain sequence. phylogenetic analysis was applied to this ests-contigs and 44 of them were found to have similarities with one of three well-known homeobox classes: bell, knox and hd-zip, and their sub-classes. however, no est-contig grouped with the fourth important homeobox class, the phd-finger homeobox. on the other hand, two sequences have showed pronounced similarity to the arabidopsis thaliana wuschel gene, considered an "atypical" homeobox gene. hierarchical clustering analysis of the expression pattern of these putative eucalyptus homeobox genes revealed the presence of ten distinct expression groups. combining phylogenetic analysis and expression patterns for some of the eucalyptus genes revealed interesting aspects about some of the potential homeobox genes, which might lead to a better understanding of the eucalyptus biology and to biotechnological applications.