Under global warming scenarios, rising temperatures can constitute heat stress to which species may differentially respond. Within a described species, knowledge on cryptic diversity is of further relevance, as different lineages/cryptic species may differentially respond to environmental change. The Brachionus calyciflorus species complex (Rotifera), which was recently described using integrative taxonomy, is an essential component of aquatic ecosystems. Here, we tested the hypothesis that these (formerly cryptic) species differ in their heat tolerance. We assigned 47 clones with nuITS1 and mtCOI markers to evolutionary lineages, now named Brachionus calyciflorus sensu stricto and Brachionus fernandoi. We selected 15 representative clones, and assessed their heat tolerance as a bi-dimensional phenotypic trait affected by both intensity and duration of heat-stress. We found two distinct groups, with B. calyciflorus sensu stricto clones having higher heat tolerance than the novel species B. fernandoi. This apparent temperature specialization among former cryptic species underscores the necessity of a sound species delimitation and assignment, when organismal responses to environmental change are investigated.