Functional mapping is a statistical tool for mapping quantitative trait loci (QTLs) that control the developmental pattern and process of a complex trait. Functional mapping has two significant advantages beyond traditional QTL mapping approaches. First, it integrates biological principles of trait formation into the model, enabling the biological interpretation of QTLs detected. Second, functional mapping is based on parsimonious modeling of mean-covariance structures, which enhances the statistical power of QTL detection. Here, we review the basic theory of functional mapping and describe one of its applications to plant genetics. We pinpoint several areas in which functional mapping can be integrated with systems biology to further our understanding of the genetic and genetic regulatory underpinnings of development.