Trichoderma species possess numerous beneficial traits and hold significant potential for agricultural applications. However, recent studies indicate a general lack of knowledge regarding the prevalence of Trichoderma species in tomato fields in Côte d'Ivoire. This study aimed to identify Trichoderma species isolated in Côte d'Ivoire with potential agricultural benefits. Ten Trichoderma morphotypes were selected based on their biostimulant performance in relation to agromorphological parameters observed in a prior study. Macroscopic and microscopic analyses, PCR, amplicon sequencing, and phylogenetic inference were employed to characterize Trichoderma species isolated from tomato fields. Three species; T. asperellum, T. virens, and T. hamatum were identified as particularly promising. Assessment of the resulting phylogenetic tree revealed similarities between these three Trichoderma species and strains isolated elsewhere in Côte d'Ivoire, Ghana, Nigeria, Kenya, Morocco, and Egypt. Detailed understanding of these promising species could contribute to improved tomato yields in Côte d'Ivoire through their application as biofertilizers and biostimulants.