We attempted to establish migratory connectivity patterns for American redstarts Setophaga ruticilla between their breeding and wintering grounds by characterizing the composition of their haematozoan parasite assemblages in different parts of their range. We detected significant but limited geographic structuring of haematozoan parasite lineages across the breeding range of the redstart. We found that redstarts from the south-eastern (SE) region of the breeding range had a significantly different haematozoan parasite assemblage compared with populations sampled throughout the rest of the breeding range. Evidence using stable isotopes from feathers previously demonstrated that redstarts from the SE of the breeding range also have a unique and separate wintering range. Thus, although two methods of estimating migratory connectivity have now both shown the SE US breeding sub-population of redstarts to be distinct from other populations on both the breeding and wintering grounds, conclusive migratory connectivity for this species as a whole could not be established.