Environment Agency experts said the non-native dikerogammarus haemobaphes shrimp had been recovered from water samples taken from the River Severn at Tewkesbury in Gloucestershire, and Bevere, near Worcester.
Further discoveries of the crustacean have also been made in two canals in Worcestershire.
While the newly-found species is related to the “killer” shrimp, which has disrupted waterway ecosystems elsewhere in Britain, experts are as yet unsure what its impact might be.
David Throup, of the Environment Agency, said: “We are concerned that this invasive species has been found in the Midlands.
“We now have a dedicated team whose focus is to establish the degree of the problem, and whether the shrimp has spread wider than the locations already found.”