Microbial pathogens cause the most economically important diseases infecting cultivated potato (Solanum tuberosum L.) in Lesotho. This study focused on the morphological and molecular characterization of microbial pathogens associated with various potato diseases. Microbial genera were isolated from potato leaves and tubers showing atypical symptoms of elephant hide, corky cracks, star-shaped lesions, circular corky lesions, raised corky spots, enlarged lenticels, and rusetting collected from naturally infested field soil. The collected isolates were cultured on Potato Dextrose Agar (PDA) for morphological characteristics such as colony color and mycelial growth pattern, with microscopic examination done for analysis of hyphal branching and the presence of constrictions. Molecular characterization was further done by sequencing the internal transcribed spacer regions (ITS1 and ITS4) of ribosomal DNA (rDNA) for fungal identification and 16S rDNA sequencing for bacterial identification and phylogenetic analysis of the identified sequences. Four important microbial pathogens identified were Fusarium oxysporum, Phytophthora infestans (late blight), Rhizoctonia solani (elephant hide and black scurf), Colletotrichum coccodes (black dot) and Fusarium oxysporum by morphological characterization, while ITS DNA sequencing was also able to identify four pathogens, Rhizoctocia solani AG 4, Neocosmospora (Fusarium) solani, Fusarium oxysporum and Fusarium longifundum associated with elephant hide, black scurf and dry rots, respectively. The most frequently isolated fungal genus from all tested isolates was Fusarium, and constituted almost 60% of the species used in pathogenicity tests in this study, with around 40% of all Fusarium isolates tested in this study caused dry rot on progeny tubers. The blemishes observed on progeny tubers were described in comparison to the original blemishes on source tubers in pathogenicity tests and most isolates failed to reproduce the blemishes of origin on progeny tubers which nullified these species as causative agents. The recovery of inoculated isolates from blemished progeny tubers was the last condition to confirm that the isolates were involved in causing blemishes. Characterization of microbial pathogens is important for accurate identification and understanding of their roles in potato disease etiology. This is the first report of tuber cracks and elephant hide caused by R. solani AG-4 and Fusarium spp. complexes causing potato root rots in Lesotho. The results will enable farmers and extension officers to formulate effective and timely control strategies against these potato diseases.