The Blue Swallow (Hirundo atrocaerulea) is a threatened intra-African migrant with breeding populations in three geographically disjunct regions. We analysed stable hydrogen, nitrogen and carbon isotope ratios in feather keratin to determine whether these vary among breeding populations, and whether feathers can be used to infer migratory connections between breeding and non-breeding areas. Blue Swallows from the three major breeding populations differed significantly in terms of their feather δD and δ15N values [South Africa/Swaziland: δD = −25.1 ± 6.7‰ Vienna Standard Mean Ocean Water (VSMOW), δ15N = 10.4 ± 1.0‰ atmospheric nitrogen (AIR); Zimbabwe: δD = −59.9 ± 7.5‰ VSMOW, δ15N = 10.1 ± 0.6‰ AIR; Malawi/Tanzania: δD = −43.2 ± 10.8‰ VSMOW, δ15N = 11.7 ± 1.3‰ AIR], but not in terms of feather δ13C. We also analysed feathers from seven individuals caught in the non-breeding range on the shores of Lake Victoria in Uganda. A discriminant function analysis assigned four of these birds to the South Africa/Swaziland breeding population and two to the Malawi/Tanzania breeding population (P > 0.997), with the remaining individual not being unambiguously assigned. Our results reveal that migratory connections in this threatened species can be inferred from feather stable isotope analysis, and that there is overlap in the wintering ranges of at least two of the three major breeding populations.