In the genus Drosophila, variation in recombination rates has been found within and between species. Genetic variation for both cis- and trans-acting factors has been shown to affect recombination rates within species, but little is known about the genetic factors that affect differences between species. Here we estimate rates of crossing over for seven segments that tile across the euchromatic length of the X chromosome in the genetic backgrounds of three closely related Drosophila species. We first generated a set of Drosophila mauritiana lines each having two semi-dominant visible markers on the X chromosome and then introgressed these doubly marked segments into the genetic backgrounds of its sibling species, D. simulans and D. sechellia. Using these 21 lines (7 segments, 3 genetic backgrounds) we tested whether recombination rates within the doubly marked intervals differed depending on genetic background. We find significant heterogeneity among intervals and among species backgrounds. Our results suggest that a combination of both cis- and trans-acting factors have evolved among the three D. simulans clade species and interact to affect recombination rate.