Abstract This study examines the hypothesis that the winter deep-dwelling and spring surface-dwelling female Neocalanus tonsus in waters off the east New Zealand coast are genetically distinct, reproductively isolated species. This is done by comparing sequences of two variable regions of DNA (16S and ITS) from winter and spring N. tonsus collected in 1996, using N. plumchrus (a northern hemisphere congener) as an outgroup. Analysis of sequence data, indicated clear genetic differences between N. tonsus and the outgroup N. plumchrus, with an average of 12% of the 16S sequence and 5.5% of the ITS sequence representing nucleotide substitutions between the two taxa. Low levels of intra-specific genetic differentiation were recorded (1% nucleotide differences among individuals); however there were no sequence differences between the N. tonsus females caught in deep water in August (winter) and in shallow water in October (spring). The morphology of these two types of females did not reveal any obvious differences. It is therefore likely that the two types do not represent different species but are ecological variants of a single species. The implications of N. tonsus being able to fuel reproduction in two different ways are discussed.