Cryptic copepod species, Pseudocalanus moultoni and P. newmani, were discriminated by PCR based on mitochondrial COI.

Cryptic species show distinct patterns of distribution and abundance on Georges Bank during January to June, 1999.

Pseudocalanus moultoni concentration in deep layers may aid retention and reduce advective loss from the Bank.

Pseudocalanus newmani concentration in surface waters makes species subject to wind-driven transport.

Discrimination of cryptic species is necessary to understand and predict changes in zooplankton diversity and pelagic ecosystem function.