Breeding data for pied flycatchers Ficedula hypoleuca and collared flycatchers F. albicollis, from 47 localities in the Czech Republic and Slovakia, were analysed. We show that co-existence and hybridization were mainly restricted to a rather narrow, latitudinal cline. The distribution of the two flycatchers coincides with topography and habitat, collared flycatchers dominating in warmer habitats than pied flycatchers. Maintained co-existence within the same locality was the exception rather than the rule and most matings occurred in allopatry. In sympatry hybridization occurred at a frequency that was much lower than expected from random mating. Hybrids had low hatching success but some hybrids were apparently fertile. Shortage of conspecific mates may explain why individual birds engage in mixed species pairs. The proportion of pied flycatchers that was involved in mixed pairs was high and increased with decreasing relative frequencies of pied flycatchers in the population. The proportion of collared flycatchers involved in mixed pairs was low, reflecting the higher relative frequency of this species in most mixed populations. Comparisons suggest that fewer hybrids are breeding in the Central European, clinal hybrid zone than in the isolated hybrid zones of the Baltic Isles. Moreover, hybrid fertility was apparently higher in the island zones than in the clinal zone. We suggest that more extensive introgression in the isolated island populations has resulted in an increase in hybrid fitness by an accumulation of fertile individuals of mixed ancestry (i.e. F2, F3 … Fn-hybrids) acting as bridges for gene exchange. Differences in the dynamics of the two classes of hybrid zones, especially in pattern of gene flow, may explain these differences in frequency and fertility of hybrids.