In vascular plant systematics there are sometimes conflicts between phenotypic and ecotypic variation and genetic differentiation that challenge species concepts, introduce taxonomic confusion, and create nomenclatural uncertainty. Until a 2014 taxonomic revision that segregated Kunzea ericoides into 10 species, it and K. sinclairii were the only species recognised in New Zealand. A recent DNA microsatellite study failed to support any of the new species, instead revealing biogeographic variation. Here we present the results of a genotyping by sequencing study with 1,361 single nucleotide polymorphisms (SNPs), sampling 48 populations representing four Kunzea species from South Island and southern North Island.