We have studied the inheritance of mitochondria in Pelargonium section Ciconium using interspecific crosses. We generated 36 different interspecific crosses. We designed KAPS markers targeting four individual mitochondrial markers, belonging to the four main crossing parents, that discriminate between an individual species and the other section Ciconium species. We found that maternal inheritance of mitochondria is most frequent, but we find occasional occurrences of paternal inheritance, while biparental inheritance is rare. For the P. multibracteatum crossing series we found ambiguous results. Our results confirm what was found before, namely that paternal inheritance of mitochondria can occur in P. sect Ciconium but that the instance is rare and much less common than is the case for chloroplasts.