A variety of gymnosperms (13 species of conifer from 5 families and 2 species of non-conifer) were collected and the small ribosomal subunit (18s rRNA) was sequenced by direct sequencing. Fifteen species were examined in the study, which included widely separated provenances of Araucaria cunninghamii, to determine the phylogenetic relationship of these gymnosperms. Two of the four conifer families found in Australia that were included in the study (Araucariaceae and Podocarpaceae) separated as expected with further separation of genera and species within these families. Homologies between the gymnosperms varied from 89% to 98%. Four geographically distinct groups within A. cunninghamii were separated phylogenetically. This study suggests that A. cunninghamii was the most recent Araucaria species to evolve, with the Papua New Guinean provenances undergoing the fastest evolutionary changes. This type of analysis has provided molecular evidence to support the taxonomy of the Coniferales. It has shown, contrary to an established understanding in angiosperms, that sequence information of the 18S rRNA genes provides a useful means of studying phylogeny in the gymnosperms at the species and within-species levels.