In this study, four species of Alternaria as A. alternata (Fr.) Keissler, A. solani (Sorauer), A. tenuissima (Kunze) Wiltshire and A. zinniae M.B. Ellis were detected in seed samples of zinnia collected from the commercial lots in Egypt. Koch’s postulates performed in pots under greenhouse conditions proved that only A. zinniae was the main causal pathogen of leaf spot. Moreover, it was frequently detected in all seed components of coat, cotyledon, and embryo. Disease severity induced by all isolates of A. zinniae was highly related to growth stages of zinnia, where it increased with the development of plant age from 1 to 8 weeks old. Transmission of A. zinniae infected seed to seedling was at 51.3% (blotter method), whereas using seedling symptom test and test tube agar method exhibited infected seedling of 58.5 and 55.8%, respectively. In the efficacy test of extracts from different materials of thuja against A. zinniae performed in vitro, leaf methanol and water extracts were the most effective treatments, where they completely inhibited spore germination at a concentration of (5 and 3%, respectively) and mycelial growth at (7 and 7%, respectively) followed by seed methanol and water extracts. In the field experiments conducted during 2016 and 2017, a highly significant reduction in the percent of leaf area infected with A. zinniae of zinnia occurred after seeds were treated by soaking in methanol extracts of 3% leaf and 7% seed for 15 min before sowing. Hence, there is a scope to integrate thuja leaf and seed extracts as plant-derived agents for eco-friendly management of A. zinniae on zinnia.