In North America, most species of the Candonidae family belong to the genus Candona . These species are frequently found in freshwater ecosystems and in sediment sequences, which makes them valuable tools for paleoenvironmental reconstructions. Knowledge of Mexican Candona species is limited, however, and scant information exists regarding their taxonomy and ecology. Here we describe Candona alchichica, a new ostracod species we suggest being endemic to Lake Alchichica, central Mexico. The species belongs to the acuminata group of species, based on the presence of 5+1 setae on the second segment of the mandibular palp. It is closely related to C. patzcuaro , C. tahoensis and C. ohioensis , but differs from those species in that the females have an elongated genital field, wide at the base and narrow at the end. Males have elongated hook-like prehensile palps and a particular arrangement of lobes in the hemipenis, i.e ., the a-lobe is inclined with a digitiform basal projection, the b-lobe is distally rounded and the h-lobe is square-shaped and exceeding the length of the b-lobe. Candona alchichica n. sp. and C. patzcuaro display very similar shells in length and morphology, which can cause confusion if identification is carried out in the absence of soft parts, a common situation when dealing with carapace and valve remains in sediment cores. Detailed morphometric analyses, however, revealed a clear difference between the valves of the two taxa. Candona alchichica n. sp. has taller valves (p˂0.05), with concave dorsal margin, and with the anterior margin considerably narrower than posterior margin, all characteristics different from C. patzcuaro. Most important, in spite of their similar shape, the two species exhibit contrasting ecological preferences. Candona alchichica n. sp. inhabits clear, cold, saline, oligotrophic waters, whereas C. patzcuaro dwells in turbid, warm, fresh, eutrophic waters. In addition, we include a revision of the morphological characteristics and taxonomic position of C. patzcuaro , based on type material and specimens collected from the type locality ( i.e ., Lake Pátzcuaro, Michoacán). This study highlights the importance of undertaking detailed morphometric analyses of the recent ostracod fauna to provide reliable taxonomic identifications and ecological characterizations of species, which are critical for accurate paleoclimatic and paleoecological reconstructions.