<p>Alternaria leaf spot and flower blight disease, predominantly caused by <i>Alternaria tagetica</i>, is the major fungal disease of marigold causing a substantial loss in both yield and flower quality across tropical, sub-tropical and humid regions worldwide. Most of the present-day marigold varieties are susceptible to the disease which is generally managed by spraying systemic fungicides. Hence, exploring host resistance and developing resistant varieties is the most economical and sustainable approach for managing the disease. The present study reports screening of 191 marigold genotypes for resistance against <i>A. tagetica</i>. Based on percent disease index and area under disease progression curve, the genotypes could be classified as moderately resistant, susceptible and highly susceptible under natural epiphytotic conditions of the field. This differential response of the host genotypes in response to the <i>Alternaria</i> infection was confirmed under artificial screening by detached leaf assay. The behavioral response of the moderately resistant and highly susceptible genotype was observed under the scanning electron microscope for the mechanism of pathogen invasion. The highly susceptible genotype exhibited increased fungal growth in terms of hyphal and conidial production, compared to moderately resistant genotype. Further, weather parameters being the determining factor for initiation and spread of disease, genotypes had differential response with moderately resistant genotypes showed greater resilience to adverse weather conditions compared to the highly susceptible genotypes. A multiple linear regression model was constructed to quantify the impact of weather parameter on the disease progression, revealing maximum temperature and rainfall as the critical factors in the spread of Alternaria leaf spot and flower blight disease. The identified moderately resistant genotypes holds substantial potential for its incorporation in the future resistance breeding program.</p>