The circadian clocks of marine zooplankton are poorly studied. With the exception of a few notable species, most zooplankter circadian clocks are uncharacterized. Well characterized clocks may shed light on ecologically relevant marine phenomena such as diel vertical migration that are suspected to be driven by endogenous pacemakers. Further, many of these species are also poorly represented in the publicly available sequence databases. To this end, we have sequenced and assembled de novo the transcriptomes of 17 diverse marine zooplankton that undergo diel vertical migration. We show that the circadian clock -- as it is known from model organisms -- appears to be largely conserved in these species.