During the past six years, 15 new seahorse species (Syngnathidae: Hippocampus) have been described on the basis of morphological characters. This approach is known to be problematic, and most species names in Hippocampus are now considered to be synonyms. Genetic methods have great potential to resolve the confused taxonomy of the genus, but none have yet been incorporated into species descriptions. In the present study, mitochondrial control region and cytochrome b DNA sequences, as well as morphological data from the recently described Queensland seahorse, Hippocampus queenslandicus Horne, 2001, were compared with corresponding data from closely related seahorse species to determine whether there is strong support for distinction of this taxon. The haplotypes of H. queenslandicus were nested among haplotypes belonging to two of the three major Southeast Asian lineages of H. spinosissimus Weber, 1913. Although incomplete lineage sorting characteristic of very recently diverged species cannot be ruled out, the genetic results suggest that H. queenslandicus is paraphyletic. Morphometric analysis further fails to provide strong support for the species status of H. queenslandicus. We conclude that support for the distinctness of H. queenslandicus is weak, and indicate that it is a synonym of H. spinosissimus. The taxonomic validity of other recently described seahorse species should be similarly scrutinised using combined genetic and detailed morphological methods.