Background and Objective: Fruits are important sources of income for farmers. However, they are subject to many diseases caused mainly by fungi, of which the genus Colletotrichum. The genus Colletotrichum is an important and frequent causal agent of post-harvest infections of fruits. Although this genus can infect a wide range of hosts, one or more species of Colletotrichum may be found on the same host. Based on morphological characteristics, this study aimed to differentiate 49 isolates of Colletotrichum sp., obtained from avocados and mangoes from the main production areas in Côte d'Ivoire. Materials and Methods: In this study, the growth rate of Colletotrichum isolates was evaluated on three culture media (potato dextrose agar (PDA), malt agar and corn meal agar (CMA) media), as well as their sporulation. The size of the spores was measured and their shapes were noted. Descending hierarchical classification (DHC) was used to group the isolates by size. A comparison of isolates obtained from the two fruits was performed by Principal Component Analysis (PCA) based on all morphological characteristics studied. Results: The study revealed a very high morphological variability in the conidia of Colletotrichum isolates. DHC grouped avocado isolates into 11 classes and mango isolates into four classes. Spore shape analysis revealed a majority of spores with either both ends rounded or one end rounded and the other sharp. Growth and sporulation of the isolates were best on the malt medium. PCA revealed that mango isolates were distinct from avocado isolates. Conclusion: This study showed that most isolates had cylindrical or ellipsoidal spores with rounded or one sharp end, with better growth and sporulation on the malt medium. However, these isolates were distinct and reported to have characteristics of Colletotrichum gloeosporioides and Colletotrichum acutatum.