A new cryptic species of Ensis from the Pacific coast of South America based on geometric morphometrics is revealed. Ensis macha (Molina, 1782) is one of the most important shellfish resources in South America. It was historically reported from San Matías Gulf, Argentina in the Atlantic Ocean to the Peruvian coast in the Pacific. A recent study analysed the intraspecific variation of this species along its distribution range and the genetic results indicated the presence of cryptic diversity. Two evolutionary clades were found: a southern clade (from cold-temperate waters) and a northern clade (from warm-temperate waters). New results based on geometric morphometrics supported the description of Ensis loboi n. sp. for the northern clade. The southern clade retains the name due to type locality of E. macha in Chiloé, Chile. The description of Ensis loboi n. sp. for the southeastern Pacific Ocean has important implications for future studies focused on fisheries management and biogeographical radiation of the group.