In this study, a new Vairimorpha isolate was defined from Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) in Turkey (Malatya). Infection was determined in the host's hindgut, both larval and adult stages. Two types spore originated from the polymorphic sporulation was detected during the observations. While the binucleate ovocylindrical fresh spores were measured 4.38 ± 0.31 μm (5.09-3.77 μm, n = 100) in length and 2.80 ± 0.18 μm (3.21-2.43 μm, n=100) in width, the ovoid meiospores were measured as 3.50 ± 0.46 μm (4.98-2.51 μm, n = 100) in length and 2.02 ± 0.28 μm (2.94-1.50 μm, n=100) in width. The multilocus genetic analyses based on SSU rRNA and RPB1 genes were carried for determining the phylogenetic status of the current microsporidium. In ML and BI trees, the current microsporidium was separated into a different branch from V. necatrix strains within the Vairimorpha clade