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<p> Abstract</p> <p>Background</p> <p>Many approaches utilize metabolic pathway information to reconstruct the phyletic tree of fully sequenced organisms, but how metabolic networks can add information to original genomic annotations has remained open.</p> <p>Methods</p> <p>We translated enzyme reactions assigned in 1075 organisms into substrate-product relationships to represent the metabolic information at a finer resolution than enzymes and compounds. Each organism was represented as a vector of substrate-product relationships and the phyletic tree was reconstructed by a simple hierarchical method. Obtained results were compared with several other approaches that use genome information and network properties.</p> <p>Results</p> <p>Phyletic trees without consideration of network properties can already extract organisms in anomalous environments. This efficient method can add insights to traditional genome-based phylogenetic reconstruction.</p> <p>Conclusions</p> <p>Structural relationship among metabolites can highlight parasitic or symbiont species such as spirochaete and clamydia. The method assists understanding of species-environment interaction when used in combination with traditional phylogenetic methods.</p>