True-breeding lines of Zinnia marylandica Spooner, Stimart & Boyle [allotetraploids of Z. angustifolia H.B.K. and Z. violacea Cav. (2n = 4x = 46)] were backcrossed with autotetraploid Z. angustifolia (2n = 4x = 44) and Z. violacea (2n = 4x = 48). Seed-generated, backcross (BC1) families were screened for resistance to alternaria blight (Alternaria zinniae Pape), bacterial leaf and flower spot [Xanthomonas campestris pv. zinniae (Hopkins and Dowson) Dye], and powdery mildew (Erysiphe cichoracearum DC. ex Merat). All BC1 families exhibited high levels of resistance to alternaria blight and powdery mildew. BC1 families derived from crossing Z. marylandica with autotetraploid Z. angustifolia were highly resistant to bacterial leaf and flower spot, whereas BC1 families derived from crossing Z. marylandica with autotetraploid Z. violacea were susceptible to this disease. Our results suggest that one Z. angustifolia genome in BC1 allotetraploids is sufficient to confer resistance to A. zinniae and E. cichoracearum, but at least two Z. angustifolia genomes are required in BC1 allotetraploids to provide resistance to X. campestris pv. zinniae.