Fungal diseases; blast, and brown spot in rice incur severe yield losses worldwide. Blast is caused by Magnaporthe oryzae, while Bipolaris oryzae is reported as the main causal organism of brown spot. Both diseases cause leaf lesions which are difficult to be differentiated by symptomatology until the late stages. Early detection and differentiation of the lesions would help the adoption of disease management strategies specific to the pathogen and will prevent the native impact on the quality and quantity of rice yields. This study was conducted in the Northern Province of Sri Lanka over five consecutive rice cultivating seasons to characterize the causal fungi of rice blast and brown spot diseases by morphological and molecular means and to develop a visual guide to differentiate the two diseases. Disease incidence was recorded in 114 fields from 2017 to 2019, and fungal isolates associated with lesions of both the diseases were cultured and subjected to morphological and molecular characterization. Competitive growth interaction between M. oryzae and the more common individual fungal isolates of the brown spot lesions, was evaluated. Fungal metagenomics analysis was conducted for the fungal spp. isolated from brown spot lesions. A suppression of blast accompanied by an increased incidence of brown spot disease was observed during the study period. M. oryzae was confirmed to be the causal organism of the blast while over 20 species of fungi were identified to be associated with brown spot lesions through morphological, molecular studies, and metagenomics analyses. Fungal ITS region sequencing revealed considerable genetic variation in the highly conserved region of DNA sequences of blast and brown spot fungal isolates. B. oryzae, Curvularia, and Microdochium species were commonly isolated from brown spot lesions. In vitro competitive growth interaction among the fungal isolates revealed growth suppression of M. oryzae by the fungal isolates associated with the brown spot lesions. Similarly, it can be speculated that the abundance and severity of blast in the field may have an influence on brown spot associated fungi. A simple visual guide was developed to differentiate blast and brown spot lesions. The findings would be highly useful in the timely management of these major fungal diseases affecting rice.