Electrophoresis, comparative morphology, and prevalence of parasites were examined in arrow squidNototodarus sloanifrom New Zealand waters. Electrophoresis revealed 2 alleles at the a‐glycerophosphate dehydrogenase locus. Specimens from eastern and southern areas of New Zealand were fixed for a slow allele and specimens from western areas were fixed for a fast allele. Two types of hectocotylised ventral arms were observed in mature males; one type was found in eastern and southern areas and die other in western areas.Nybeliniasp. post‐larvae showed high infestation levels in western squid, but none were found in eastern and southern specimens. It is concluded that there are 2 species of arrow squid in New Zealand and that these are associated with the major water masses. Some overlap between the species was found in fishery areas Cook Strait, Tasman Bay, and Egmont.