Autecologic information of aquatic insects in the river systems under extreme continental climatic conditions is limited. Therefore, the objective of this study was to analyze life cycles, larval development, densities, microhabitat distribution, and secondary production of two sympatric burrowing mayfly species, Ephemera orientalis and Ephoron nigridorsum, in the Kharaa River, Northern Mongolia. Both species were typically distributed within the middle reaches of the focus river, displaying significant different larval densities across the three study sites. Four distinct microhabitats for E. orientalis and E. nigridorsum were identified. The preferred habitats of both species were substrates composed of rocks, cobbles, or coarse gravels with variable smaller mineral fractions of finer sandy, muddy, or organic substrates beside. Based on larval body size distribution and the emergence period, it was concluded that E. orientalis has a univoltine winter life cycle. The estimated annual production of larvae at two investigated sites in the middle stretch of the river in the year 2009 was 1.65 and 2.25 g DW m⁻² year⁻¹. Biomass was 294.8 and 490.3 mg DW m⁻², and the annual production to biomass rate (P/B) was 4.5 and 5.6 year⁻¹, respectively. In contrast, E. nigridorsum displayed a univoltine summer life cycle with a very likely egg diapause of approximately 8 months. Annual production estimates were 5.27 and 7.89 g DW m⁻² year⁻¹, biomass was 281.2 and 443.2 mg DW m⁻²; the annual P/B rates were 17.9 and 18.7 year⁻¹ at the two sites reflecting the extremely shortened life cycle of this species. We conclude that the two sympatric species showed a difference in life cycles but no separation in habitat selection.