Histomonas meleagridis and Tetratrichomonas gallinarum are two protozoans responsible for mortality associated with typhlohepatitis in poultry. In this study, the etiology of high mortality in Chukar partridges suspected of infection with these agents was investigated pathologically and molecularly. Twelve healthy partridges during the laying period and 30 partridges that died due to disease and were included in the study. In blood analysis, increased levels of WBC, NEU, LYM, MONO, EO and BASO suggesting bacterial and/or parasitic infection; decreased levels of HGB, MCH and MCHC, which are markers of anemia; and increased AST and LDH levels, which are important for liver degenerations. In the liver, which is one of the most pathologically affected organs, multifocal necrosis foci that sometimes merge with each other and spread to large areas, and severe fibrino-necrotic typhlitis were detected. There was amyloid deposition in the space of Disse and vascular sinuses in the liver. PAS positive protozoal agents were observed in and around the lesioned areas. By PCR analyzes using specific primers, 11 of the samples were positive for H. meleagridis only, whereas 5 were positive for T. gallinarum only; 14 samples tested positive for both agents. Sequence analysis showed 100% identity between all samples resulting in positive PCR. In addition, Escherichia coli was produced in microbiological culture (27 of 30). When all the results were evaluated together, it was concluded that H. meleagridis and T. gallinarum and secondary E. coli may cause high mortality in partridges under lay stress.