This study aims to assess the morphological, cultural, and microscopic diversity of Lasiodiplodia sp. isolates from woody and fruit crops in Côte d’Ivoire, to better understand their variability and support integrated fungal disease management. It is a descriptive and experimental study conducted at the phytopathology laboratory of the Institut National Polytechnique Félix Houphouët-Boigny (INP-HB) in Yamoussoukro, with surveys carried out in the main agricultural areas. A total of 281 symptomatic samples were collected from seven economically important crops (cashew, mango, cacao, cola, rubber, Polyalthia longifolia, and banana) in 96 locations. Isolates were purified on various media (PDA, CMA, and agar), and 161 representative isolates were selected for morpho-cultural and microscopic evaluation. Characteristics studied included mycelial growth rate, colony appearance, pycnidia count, and conidia size, shape, color, and density. Statistical analyses were performed using XLSTAT (one-way ANOVA, Newman-Keuls test, p < 0.05). The results revealed strong morpho-cultural variability depending on the host, culture medium, and agroecological zone. Radial growth rates ranged from 1.45 to 6.04 cm/d, and three colony morphotypes were identified (grayish, brown, and blackish). The mean number of pycnidia ranged from 0 to 7.00. Conidia were ovoid, ellipsoid, or oblong, measuring 4.81–18.29 µm × 2.95–10.53 µm, with spore densities ranging from 0.90 to 50.00 conidia/ml. The proportion of unicellular and bicellular conidia differed depending on the isolate and host. Statistical analysis confirmed that the host and the medium significantly influenced colony and spore morphology. This morpho-cultural and microscopic diversity underscores the combined influence of the host, the environment, and agroecological conditions. The results provide an essential basis for understanding pathogenicity and implementing integrated management strategies for fungal diseases in woody and fruit crops in Côte d'Ivoire.