A new species, Conioscypha peruviana was isolated from submerged woody debris collected in streams, rivers and a swamp in Peru. The anamorph formed in culture and morphological and molecular data support the inclusion in the genus. A phylogeny generated with maximum likelihood and Bayesian approaches placed the fungus in a well-supported clade with other Conioscypha and Conioscyphascus species. Nomenclature used herein reflects changes made in the Melbourne Code, with Conioscyphascus being considered a later synonym of Conioscypha. The fungus is described, illustrated and compared to morphologically similar taxa. In addition, Conioscypha gracilis comb. nov. is identified from both lentic and lotic habitats in Peru.