The vigorous burrowing activities of many thalassinidean shrimp have such dramatic effects on their habitats of soft sediment that these animals are often considered ecosystem engineers. Because they strongly interact in these communities, basic information about their life histories and population dynamics is needed to effectively manage the habitats in which they live. These data can only be obtained if the shrimp can be accurately identified. On the west coast of the United States, two species of burrowing intertidal shrimp in the genus Neotrypaea, N. californiensis and N. gigas, often co-occur and are not easily differentiated morphologically except as adult males by characters of the major claw (which is often lost in collection). Here we describe and validate (using mtDNA data from the cytochrome b gene) an allozyme marker (LDH) that can be scored rapidly and inexpensively for the identification of these species. We used this marker to generate a large sample of molecularly-identified specimens that we then used to evaluate a variety of morphological characters in an effort to differentiate the two species. With the exception of characters associated with the male major claw, most of the morphological characters examined here were not useful in distinguishing members of the two species. The exceptions were two simple and robust characters associated with the eyestalks—length, and shape of the distal outer edges. These could be used to reliably differentiate between the two species regardless of sex, and over a wide range of sizes. We hope that these characters will facilitate future studies of the distribution, habitat preference, and comparative biology of these two often co-occurring species.