Ethanol is one of the most commonly used fixatives for zooplankton samples in molecular studies, despite known problems with this method. Alternative preservation solutions are desired that would reliably preserve DNA over medium to long time scales (months to years). This study tested the efficacy of acetone as a bulk fixative for DNA preservation in marine zooplankton. We used quantitative polymerase chain reaction to measure changes in DNA copy number individual−1 over weeks to months in specimens of the planktonic copepod Parvocalanus crassirostris that were bulk preserved in (i) acetone, with the fixative changed within 24 h of collection, (ii) acetone, with the fixative not changed and (iii) a standard 95% ethanol bulk fixation protocol. We found that DNA preservation in acetone was comparable to that in ethanol in both short- (30 days) and long-term (4 months) laboratory and field experiments, with modest, but non-significant, declines in DNA copy number individual−1 over time. Significant DNA degradation was observed over a 4-month storage period in acetone-preserved samples in which the fixative was not changed immediately following collection. Although acetone provided comparable DNA preservation to ethanol in this study, we also found that precipitates form in the presence of seawater, making identification of copepod specimens difficult in bulk acetone preserved samples. For this reason, we do not recommend acetone as a bulk fixative, but do recommend that it be considered a good alternative for preservation of individual specimens in taxonomic groups that are known to preserve poorly in ethanol (e.g. chaetognaths).