Hemichordates, especially enteropneust worms, have become increasingly important in phylogenetic studies to test theories of chordate evolution. However, there are many populations of enteropneusts along the Pacific Northwest coast of North America that have not been identified. Here we show that two common Pacific Northwest enteropneust species, Saccoglossus pusillus and Saccoglossus bromophenolosus, can be distinguished by both morphological and molecular characters, and we identify several populations of both species. We compare them with a closely related species, Saccoglossus kowalevskii, from the Atlantic coast of North America. We compile the morphological characters used to distinguish harrimaniid enteropneusts, and we describe a new staining method to examine the gill bars and proboscis skeleton of enteropneusts to aid in identification. Using 18S and 16S ribosomal DNA sequences, we determine that the range of S. pusillus extends from southern California, where the worm was first identified, to southern Canada. This previously unknown large range shows a dramatic geographic cline in adult body size, with the smallest populations found in the south and the largest adults near Vancouver Island. In contrast, S. bromophenolosus may be a Pacific Northwest species that was relatively recently introduced from the Atlantic Ocean.