In all, 50 isolates of Fusarium graminearum from wheat spikes in New York, including 25 isolates each of the 15-acetyl-deoxynivalenol (15-ADON) and 3-ADON genotype, were tested to determine whether 3-ADON isolates are more fit for saprophytic survival and pathogenicity on wheat spikes than are 15-ADON isolates. The isolates were characterized and compared for 14 different attributes of saprophytic fitness and pathogenic fitness on a susceptible wheat variety. Isolates of the two genotypes could not be differentiated for most of these traits. Three principle components—ascospore production on corn stalks, total trichothecene amount in wheat kernels, and incidence of diseased spikelets up from the point of inoculation—accounted for 29.4, 18.9, and 10.8% of the variation among the isolates, respectively. A bootstrapping procedure grouped the isolates into two distinct groups, with 27 and 23 isolates each, with isolates from both genotypes represented in similar proportions (15-ADON/3-ADON, n = 14/13 and 11/12). Within the contemporary population of F. graminearum causing wheat head blight in New York, isolates with a 3-ADON genotype did not possess any detectable advantage over isolates with a 15-ADON genotype in saprophytic fitness or in pathogenic fitness on a susceptible wheat cultivar.