This project estimates historical recombination rates of the Eurasian blackcap (Sylvia atricapilla) and the garden warbler (Sylvia borin) using a linkage disequilibrium-based approach. The population-scaled recombination rates were inferred using 'pyrho' considering the population's demographic information and mutation rates. The mutation rate was taken from a closely related species (flycatcher, Ficedula albicollis). Here we report the recombination rate per site per generation (r, output of pyrho) for all the chromosomes along the genome for both species. Blackcap dataset file: WholeGenome_chromosomes_blackap_n38_Pen20_W50.gz Garden warbler dataset file: WholeGenome_chromosomes_SylBor_n10_Pen20W50.gz Additionally, we annotated the blackcap genome to evaluate the association between recombination rates and specific annotation features (e.g., genes, transcription start sites, promoters, 5'UTR, and 3'UTR regions). The annotation of the genome was based on RNA-seq and Iso-Seq data. It can be found with the name bSylAtr1.1.gff.