White clover (Trifolium repens L.) is a highly outcrossing heterozygous allotetraploid species, for which classic inheritance studies have been inconclusive. With the aid of molecular markers, it is now possible to study the genes controlling morphological traits. The objectives of this study were to catalog the leaf marks in white clover and map the location of leaf morphological traits based on cosegregation with molecular markers. A mapping population segregating for eight morphological traits consisting of leaf marks and number of leaflets was developed and phenotyped at two different locations during the summer and winter seasons. A confirmation population, derived by selfing one of the mapping population parents, was produced and phenotyped in one location at two different times of the year. Through the use of previously published simple sequence repeat (SSR) marker maps, linkages between the mapped molecular markers and genes for three different morphological traits was identified. The red midrib and red fleck traits were found to be controlled by two closely linked dominant genes on linkage group (LG) B1. The trifoliolate trait is controlled by at least one gene on LG H1. The identification of molecular markers linked to loci affecting leaf morphology traits resolves conflicting hypotheses on the genetics of these complex traits and has potential for molecular breeding improvement of white clover.