Molecular marker loci were used to investigate the inheritance of morphological traits that distinguish maize (Zea mays ssp. mays) from a closely related wild relative, teosinte (Z. mays ssp. mexicana). Regression and interval mapping analyses gave largely congruent results concerning the numbers of loci controlling the morphological traits and the magnitudes of their effects; however, interval mapping tended to give larger estimates for the magnitudes of the effects of the morphological trait loci. This tendency was exaggerated for traits that were non-normally distributed. Variation for most inflorescence traits is controlled by one or two regions of the genome with large effects plus several other regions with relatively small effects. As such, the data are congruent with a mode of inheritance for most traits involving one or two major loci plus several minor loci. Regions of the genome with large effects on one trait consistently had smaller effects on several other traits, possibly as a result of pleiotropy. Most of the variation for the dramatic differences in inflorescence morphology between maize and teosinte is explained by five restricted regions of the genome. One of these regions encompasses a previously described gene, tb1 (teosinte branched), and the effects of this region on inflorescence architecture are similar to the known effects of tb1. Implications of this work for the genetic basis of morphological evolution in plants are discussed.