Migratory species are of increased conservation concern because of their reliance on multiple, geographically disjunct habitats. An understanding of how long-term ecological processes and contemporary population genetic patterns are related is critical for effective management and conservation of such species. Combining traditional long-term census and mark-recapture data with temporally focused molecular genetic data can help inform these efforts. We used 24 years of banding data, 15 years of migration counts, and molecular genetic data from 17 microsatellite loci to describe the migration phenology, direction, and population connectivity of Red-tailed Hawks (Buteo jamaicensis) migrating through the Marin Peninsula, California. Count data indicated two distinct peak periods of movement across years: 15 August-30 September and 1 October-30 November. Band-encounter data from these two periods revealed a significant difference in movement: individuals in the early period of migration (15 August-30 September) displayed little net movement, whereas individuals from the second period (1 October-30 November) showed directional, southward movement. Finally, molecular genetic data suggest that the early-season period primarily involves a population from central California, whereas the second period includes both individuals from central California and individuals from desert regions of the Intermountain West. These analyses provide important information for interpreting long-term Red-tailed Hawk count and banding data and offer an example of how traditional population-monitoring methods can be combined with molecular genetic markers.