Abstract Recombination rate is heterogeneous across the genome of various species and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine‐scale population recombination rate based on the patterns of linkage disequilibrium across the genomes of multiple populations of two closely related flycatcher species ( Ficedula albicollis and F. hypoleuca ). This revealed an overall conservation of the recombination landscape between these species at the scale of 200 kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years). Genetic diversity and differentiation were associated with recombination rate in a lineage‐specific manner, indicating differences in the extent of linked selection between species. We detected 400–3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands ( CGI s), regardless of whether CGI s were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements ( TE s), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGI s are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TE s and fine‐scale variation in recombination rate may be associated with the evolution of the epigenetic landscape.