The use of molecular markers in combination with greenhouse screens provides an efficient method for identification of flue-cured and burley tobacco genotypes resistant to several diseases. The objective of this study was to compare the consistency of each method for testing resistance to black shank and black root rot, diseases caused by two distinct soil-borne fungal pathogens. The roots of four week-old seedlings were inoculated with each pathogen and at least two resistant and susceptible control lines were included for each pathogen trial. For black shank disease evaluations, plants were inoculated with either zoospores or chlamydospores and there were no observable differences between the disease development within the genotypes tested. The majority of the lines were selected as being resistant or susceptible for each disease by marker-assisted or greenhouse screening alike. However, in the case of black shank, inoculation with the pathogen (Phytophthora nicotianae race 0) gave insight into the presence of genotypes that were likely to be segregating recombinants by showing signs of partial resistance, due to the polygenic nature of existing resistance to black shank. It was useful to include the pathogen screenings in order to confirm the marker selection and to recognize lower resistant gene frequency in some of the lines prior to final testing in field disease nurseries.