Information on local recombination rates across a genome and its correlates can yield insights into the processes leading to adaptation or speciation. We generated a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using apx. 160 SNP markers distinguishing two inbred lines surveyed in apx. 1350 backcross progeny. We observed significant heterogeneity in fine scale recombination rates across these chromosomes. Additionally we detected a significant correlation between fine-scale recombination rates in adjacent windows, indicating broader scale patterning of recombination rate. We also examined how recombination rates vary with other genomic patterns such as nucleotide diversity within species, divergence to D. miranda, and sequence motifs. We found a significant relationship between recombination rates and intergenic region diversity, but no relationship between recombination rate and between species divergence. These results are consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining patterns of variation within species. We further found significant associations of fine-scale recombination rate with particular sequence motifs in some parts of the genome. Finally, we observed that fine-scale recombination rates in D. persimilis are strongly correlated with those obtained from a comparable study of its sibling species D. pseudoobscura.