Technical Abstract: Sclerotia of the soilborne plant pathogen, Sclerotinia sclerotiorum, were collected from 1 m2 area of the top 1.27 cm layer of soil in an alfalfa field. Out of 272 sclerotia collected, 40 were randomly selected and analyzed for genetic diversity in terms of microsatellite loci, mycelial compatibility groups (MCGs) and phenotypic diversity using five phenotypic traits (fungicide sensitivity, oxalic acid production, growth rate, colony color and virulence). Sixteen microsatellite haplotypes and 15 MCGs were found among the 40 isolates. The isolates showed three colony colors (beige, black and white) on potato dextrose agar and exhibited significant differences in growth rate, oxalic acid production, and sensitivity to three fungicides, benomyl, fluazinam and iprodione. In spite of the genotypic and phenotypic diversity among the isolates there was no significant difference in virulence in detached leaf assays. No apparent relationship among the neutral genetic markers and the phenotypic traits was detected. Several lines of evidence show high levels of genetic diversity and frequent outcrossing within the population of S. sclerotiorum: 1) high likelihood of five genetic populations based on Bayesian probability; 2) random association of alleles between every pairwise linkage disequilibrium test among eight independent microsatellite loci, as well as in multilocus analysis when subpopulations were defined; 3) discordances between microsatellite haplotypes and MCGs, and 4) lack of correspondence among the genetic markers and phenotypic traits. Multilocus Index of Association analyses with and without specification of subpopulations suggested outcrossing occurs only within interbreeding subpopulations of S. sclerotiorum.