Mastigoteuthid squids are ecologically important, being prey to many apex predators, yet the diversity and systematics of the family remain poorly understood. Delicate by nature, they are often damaged during capture; this has led to a controversial and unstable taxonomy for this family. Recent reviews have accepted one or two genera, and eight to 17 species. A complete taxonomic review of the New Zealand mastigoteuthids is undertaken here first time. A morphological revision of New Zealand material was completed to identify and describe locally occurring species, and to re-evaluate the status of the genera in this family. Morphological examinations focused on both internal and external anatomy. A set of morphological characters have been identified to distinguish five genera: Mastigoteuthis [Mt.], Idioteuthis, Mastigopsis [Mp.], Echinoteuthis, and Magnoteuthis [Mg.]. Eight species were identified: Mt. dentata, Mt. psychrophila, Mt. sp. X, Mt. sp. Y, I. cordiformis, Mp. hjorti, Mg. sp. nov., and E. famelica. The Mastigoteuthidae now appears to be second most diverse squid family in New Zealand waters.

Three mitochondrial genes (16S rRNA, 12S rRNA and cytochrome c oxidase subunit I [COI]) were analysed for eight different species, in order to assess the utility of DNA barcodes to differentiate between species and to test the morphological hypothesis for the division of the five genera. Genetic evidence was found that supports Mg. sp. nov. as a distinct species that has been previously misidentified as the morphologically similar species Mg. magna. Each species analysed herein exhibited unique mitochondrial DNA haplotypes for all genes, and the morphological distinction between the genera was strongly supported using a combined phylogeny with all genes. However, I. cordiformis grouped with the chiroteuthids. Of the three genes examined, the DNA barcode region shows the greatest divergence between species and should be used in future systematic work on the Mastigoteuthidae.

Because most mastigoteuthid specimens are badly damaged, integrative taxonomy is especially important for this family. Unfortunately, most specimens are formalin fixed, rendering DNA extraction difficult or impossible. Therefore, some preliminary tests were conducted on DNA from formalin-fixed museum specimens. Two sequences were recovered out of eight specimens tested using a silica-gel column-based extraction, with critical-point-dried tissue and a DNA purification protocol. The third sequence was recovered using an alkaline lysis extraction, with non-critical-point-dried tissue and without DNA purification. The sequences that were recovered showed a close relationship between Mt. agassizii, Mt. dentata, and Mt. sp. X.

Idioteuthis cordiformis is the largest mastigoteuthid squid species and may currently be facing the potential of a local extinction in New Zealand; however, its ecology has not been previously studied. Therefore, stable isotopes 15N and 13C were analysed to find the trophic position and the source of carbon, respectively, and gut contents were examined using DNA barcoding. Stable isotopes revealed a correlation between δ15N and δ13C values, and I. cordiformis δ15N indicated that it occupies a high trophic position. Morphological analysis was not successful in identifying prey items below class, while DNA barcoding was able to identify two prey species: snapper (Lutjanus sp.), and birdbeak dogfish (Deania calcea).

Although a review of the systematics of the New Zealand Mastigoteuthidae has been completed, a full review of this family is still required; an integrative taxonomic approach will be essential because there is often low interspecific and high intraspecific morphological variation. This will require continued collection efforts for new specimens, along with further research into DNA extraction from formalin-fixed tissue. In addition, future studies should also focus on the dietary habits and trophic position of mastigoteuthids in order to better understand their ecological importance.