Daphnia and other zooplankton often harbour substantial intraspecific diversity in migration behaviour. One example is partial diel vertical migration (DVM), wherein a portion of the population migrates vertically at night while another portion remains deep in the water column. This behaviour is widespread among aquatic invertebrates and can strongly influence interspecific competition. However, the mechanisms maintaining partial DVM in zooplankton are poorly understood. Here, we take an observational approach to identify the likely mechanisms maintaining partial DVM in a natural population of Daphnia pulicaria. The Daphnia at our study site show intraspecific diversity in body hemoglobin (Hb) concentration. This variation serves as a marker for differential use of a deep low-oxygen layer, which allows us to concurrently examine the relationships between individual state, genotype, and migration behaviour within the population. We found that migration behaviour within Hb-rich and Hb-poor Daphnia was not related to individual size. Furthermore, Hb-rich and Hb-poor individuals were present within all commonly found genotypes. Thus, partial DVM in the population is neither a state-dependent behaviour based on size, nor the result of a genetic polymorphism. Characterizing partial DVM provides a more precise picture of aquatic ecosystems which can strongly influence estimates of population growth and trophic interactions.