In New Zealand, Kotatea aurantiaca and Kotatea lobata are two common, endemic, co-occurring, and morphologically similar soft coral species that currently cannot be distinguished without microscopic examination of sclerites and of which little is known regarding any aspect of their ecology or biology. The aim of the present study is to ascertain if, and in what ways, their colony growth forms differ, and to test the taxonomic value of macroscopic morphological character measurements using statistical discrimination analyses. A binary logistic regression model is developed whereby macroscopic characters of colony morphology can be used to assign specimens to either species with ~ 90% accuracy. Species assignment accuracy is greatest when ratios formed from morphological measurements are used rather than direct measurements. Here, these ratios are used for the first time to account for the appearance-altering habit among soft corals of hydrostatically expanding and contracting their coelenteron with seawater. Relationships between colony morphology and depth are also examined, and it is suggested that phenotypic plasticity detected in K. lobata, causing it to resemble K. aurantiaca more closely at greater depths, may contribute to their morphological overlap. It is anticipated that this discrimination technique will facilitate future research on the ecology and biology of these species and will be replicated on other sets of morphologically similar soft corals for which species discrimination has been problematic.