Black shank, caused by the oomycete <i>Phytophthora nicotianae,</i> is an important disease of tobacco in most tobacco growing regions. Several disease management strategies are available for disease control, but they often place selection pressure on the pathogen population to adapt<i>. Phytophthora nicotianae</i> has a high level of genotypic diversity that allows the population to quickly adapt to changes in the host and environment. In this study, the level of genetic diversity and the geographic patterns associated with genotype distribution were determined for populations of <i>P. nicotianae </i>in tobacco regions of NC, KY, VA, and GA. A total of 453 isolates were collected from infested tobacco fields. Five genes, ITS46, beta-tubulin, elongation factor, NADH, and COXII, were sequenced in each isolate and used to find single nucleotide polymorphisms (SNPs) among individuals. The greatest numbers of SNPs were found in the COXII region for isolates from NC and VA, and in the EF region for KY and GA isolates. Genotypic variability was high, with multiple genotypes recovered in each state. The level of detected genetic variation was highest in GA with one new clade for every 10 isolates, one new clade for every 14 isolates in VA, and a new clade for every 22 isolates in KY. The high level of diversity found among isolates may help the pathogen population quickly shift to adapt to changes in host and environment and influence management decisions.