Background ad objective: Among the notable achievements of the twentieth century was the discovery and identification of new drugs from plants against microbial infections. However, the discovery of novel drugs since then is inadequate due to emergence of resistant microbes. In an effort to discover novel drugs, the study aimed to investigate the antimicrobial activity of crude extracts from endophytic fungi isolated from Cnidoscolas aconitifolius and Ocimum suave. Methods: Following morphological characterization and initial screening for antimicrobial activity, isolates that had higher inhibition were genotypes by Sanger sequencing. Two isolates (Candida tropicalis from O. suave and Phyllosticta capitalensis from C. aconitifolius) were tested for antimicrobial activity against