Partial migration, whereby populations consist of residents and migrants, is common among migrating organisms. Partial migration of aquatic organisms, however, remains largely under-studied even though many aquatic animals exhibit horizontal and vertical migrations during their lifetime. Macroinvertebrates of the genus Mysis exhibit diel vertical migrations (DVM). Some species have recently been observed to exhibit partial diel migrations where some individuals reside on the bottom throughout the night while others migrate into the water column. To test the hypothesis that individuals are fixed as residents or migrants, we compared demographic information and C and N isotope compositions of M. diluviana caught at night in pelagic and benthic regions of Lake Champlain. Our results suggest there are two distinct ecotypes of M. diluviana separated by migration behavior. The migrating ecotype was smaller than the resident ecotype and enriched in δ15N while the resident ecotype had a higher C:N ratio. Because we did not allow for gut evacuation prior to our analyses, we conducted a follow-up experiment to test the effect of gut content on isotope composition of M. diluviana. The experiments confirmed that differences between benthic- and pelagic-caught M. diluviana were not a result of gut contents at the time of capture. Fixed partial migration behavior in M. diluviana in Lake Champlain indicates that DVM of M. diluviana may be more complex than previously thought. Additionally, partially migrating Mysis spp. may represent a model study organism to test hypotheses about the causes and consequences of partial DVM behavior in aquatic invertebrates.