The genetic structure of complex agronomic traits in alfalfa (Medicago sativa) is not well understood. By crossing the subspecies M. sativa subsp. falcata and M. sativa subsp. sativa, a fullsib F1 population was created from which a genetic linkage map of each parental genome was developed using RFLP and SSR markers. These maps include simplex, duplex, and simplex-simplex alleles along with a number of alleles exhibiting segregation distortion. The inclusion of these more complicated segregation ratios resulted in greater saturation of the genome, a better convergence to eight consensus linkage groups, and a more realistic view of regions of the genome that may not behave normally due to segregation distortion than would have been possible by only using simplex alleles as has been done previously. The population was clonally propagated and grown at three field locations with phenotypic data collected over three years for various agronomic traits, including biomass production, forage height, and forage regrowth. Combining the marker data with the phenotypic data, markers were identified from each parental genome that were associated with these traits, suggesting that both major germplasm sources of cultivated alfalfa contain alleles that may contribute to improved alfalfa cultivars. These results provide a much better understanding of the genomic regions underlying these traits and are an important start in efforts aimed at the use of marker-assisted selection for the improvement of alfalfa cultivars.