Physic nut (Jatropha curcas L.) has emerged as a promising fruit crop in Ecuador, but the recent identification of rust poses a potential threat to its productive development. This study focused on elucidating the morphological aspects of the basidiomycete and assessing rust intensity across different canopy levels of physic nut hybrids and genotypes under field and semi-controlled conditions in Manabí, Ecuador. For the first time, this study confirms that Phakopsora arthuriana should be responsible for rust on physic nut in Ecuador based on the characteristics of the fungal structures. Rust incidence was 100% across all canopy layers, with the lower and middle canopies exhibiting higher severity and lesion numbers than the upper canopy. Using the Weibull nonlinear distribution model, we epidemiologically modeled disease progression, revealing that hybrid JAT 001100 displayed the highest temporal progress, recording 15% severity and an area under the disease progression curve of 3228.9 units. Promising genotypes CP-041 and CP-052 demonstrated lower rust intensity. Environmental parameters, including dew point, temperature, precipitation, and relative humidity, were correlated with rust severity and lesion numbers. In greenhouse assays, hybrid JAT 001165 showed higher severity, whereas JAT 001103 and JAT 001164 had more lesions than other genotypes. In contrast, promising genotypes CP-041 and CP-052 consistently exhibited lower rust intensity in both field and greenhouse environments. This study demonstrated that P. arthuriana could be epidemiologically modeled with the Weibull model, providing crucial insights into the dynamic interplay between rust infection and physic nut hybrids and genotypes under diverse conditions in the Manabí region of Ecuador.