Chromosomal rearrangements may directly cause hybrid sterility and can facilitate speciation by preserving local adaptation in the face of gene flow. We used comparative linkage mapping with shared gene-based markers to identify potential chromosomal rearrangements between the sister monkeyflowers Mimulus lewisii and M. cardinalis, which are textbook examples of ecological speciation. We then re-mapped quantitative trait loci (QTLs) for floral traits and flowering time (pre-mating isolation) and hybrid sterility (post-zygotic isolation). We identified three major regions of recombination suppression in the M. lewisii x M. cardinalis hybrid map compared to a relatively collinear M. parishii x M. lewisii map, consistent with a reciprocal translocation and two inversions specific to M. cardinalis. These inferences were supported by targeted intra-specific mapping, which also implied a M. lewisii-specific reciprocal translocation causing chromosomal pseudo-linkage in both hybrid mapping populations. Floral QTLs mapped in this study, along with previously mapped adaptive QTLs, were clustered in putatively rearranged regions. All QTLs for male sterility, including two underdominant loci, mapped to regions of recombination suppression. We argue that chromosomal rearrangements may have played an important role in generating and consolidating barriers to gene flow as natural selection drove the dramatic ecological and morphological divergence of these species.