Parthenogenetic and sexual reproduction co-occur in many animals. In such groups, determination of the timescale over which parthenogenetic lineages can persist and provide an advantage over sexual reproduction is of considerable importance, as the adoption of either reproductive mode will confer various, but conflicting, adaptational advantages. Data derived from a survey of ostracod valves preserved in 34 Holocene freshwater sediment cores suggest that environmental fluctuations during a period of less than 5000 years were sufficient to provide an advantage to sexually reproducing ostracods over parthenogenetic forms. In addition, asexual species were found not to have colonized water bodies earlier than sexual forms, nor to have persisted for longer. When viewed over timescales such as these, subfossil Ostracoda offer little support for the `general purpose genotype' hypothesis of parthenogenesis, and also suggest that the short-term costs of sexual reproduction are rapidly outweighed by its advantages in a changing environment.