The application of marker assisted selection (MAS) in plant breeding offers unique opportunities to improve the effectiveness and efficiency of selection, and address the improvement of intractable traits. The specific DNA marker system employed for MAS impacts both the effectiveness and efficiency of selection. The preferred marker system will depend upon the crop species, instrumentation available to the breeder, and the sophistication of the laboratory. For MAS, the breeder is generally running relatively few markers (i.e., limited multiplexing) on a large number of individual plants or lines. Issues such as DNA quality, DNA quantity, genotype throughput, and automated data collection and scoring become important considerations when choosing a DNA marker system. In the University of Georgia soybean improvement program the application of MAS is evolving from the use of SSR (simple sequence repeat) markers to SNP (single nucleotide polymorphism) markers. The rationale for the utilization of SNP markers includes: i) availability of robust SNP assays, ii) affordable SNP detection instrumentation, and iii) reduced cost per selected genotype when compared with SSR assays. One of our first applications of SNP-based MAS was for the Rmi gene conditioning resistance to southern root-knot nematode. For several years we had utilized the linkage of SSR markers Satt358 and Sat_132 to the Rmi gene on Linkage Group O as the MAS criterion. By January 2004 we had identified several SNP markers in the Rmi region and developed robust assays for their detection. A comparison of four flow cytometric SNP detection assays run on a Luminex 100 flow cytometer indicated the direct hybridization method of SNP detection required less time and was more cost effective than allele specific primer extension, single base chain extension, or an oligonucleotide ligation assay. In addition the direct hybridization assay was equally robust to SSR assays and cost less per genotype.