Coccidian parasites, especially Isospora, are prevalent parasites in Passeriformes. Isosporan oocysts from common mynahs (Acridotheres tristis) are incompletely described. Detailed knowledge on biology, prevalence, pathogenesis and treatment of avian isosporiasis is scant. In this study, isosporan oocysts isolated from common mynahs were morphologically and molecularly characterized. The medication efficiencies of diclazuril and sulfadiazine-trimethoprim in isosporiasis in naturally infected mynahs were evaluated. Isosporan oocysts from common mynahs were described morphologically by microscopic imaging. The 18S rRNA and COI genes were amplified using PCR and the resultant products were sequenced and analysed phylogenetically. To evaluate the efficiencies of diclazuril and sulfadiazine-trimethoprim, two experimental treatment groups and a null control were assigned. General health status, weight and oocysts per gram of faeces were evaluated. Oocysts from all birds contained isosporan oocysts that were morphologically and dimensionally similar (P < 0.05). The oocysts were spherical; with no oocyst residuum, micropyle or polar granules. At both loci, phylogenetic analyses placed the Isospora isolate in the same clade with Isospora spp. from other Passeriformes. Both of the anticoccidials were well tolerated by the birds, a rapid reduction in oocyst excretion was noted at the commencement of treatment and 72 h after drug administration, oocyst excretion zeroed in all treated birds. Based on morphological and molecular data, this isolate does not resemble any previously described isosporas, hence Isospora tristum n. sp. is proposed for the current species. Both evaluated anticoccidials seemed to be efficient in reduction of oocyst production and can be recommended for the treatment of mynah isosporiasis.