Two closely related interfertile monkeyflowers, M. guttatus and M. laciniatus occur within meters of each other and are known to hybridize, yet they maintain phenotypic and ecological divergence despite this ongoing gene flow. Previous studies have identified five major QTLs controlling for traits that assist with adaptation to the unique ecotypes in this environment. However, we conducted a Fst analysis and found the genetic architecture of divergence to be genetically complex. This homogenous pattern of genomics is in contrast to the expected simple architecture of genomic islands of divergence as suggested by the QTL analyses. In light of these results, we hypothesize that local adaptation between neighboring monkeyflowers is driven by divergent selection on many loci of small effect dispersed throughout the genome.