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Abstract The decorator wormDiopatra cupreaBosc, 1802 (Annelid; Polycheate; Onuphidae) is an ecosystem engineer within high-salinity estuaries of the southern and eastern United States. A previous study revealed five morphologically cryptic mitochondrial lineages across its broad geographic distribution. Here, we explore mitonuclear concordance of these lineages using single nucleotide polymorphisms (SNPs) genotyped with RADseq. We genotyped 3,162 SNPs from 233D. cupreaand detected four deep lineages in the nuclear genome: a northern US clade (Massachusetts), a single nuclear clade within mid-Atlantic populations (i.e., Virginia south through northeastern Florida), a southeastern Florida clade, and a Gulf of Mexico clade. There was mitonuclear concordance within most individuals for three lineages, while two mitochondrial lineages were detected in a single mid-Atlantic nuclear lineage. Thus, there appear to be four cryptic lineages ofD. cupreathat suggest four distinct species that rarely hybridize. Within the mid-Atlantic lineage, we detected increasing genetic isolation of populations with increasing geographic distance, a pattern consistent with low dispersal ofD. cuprealarvae. Cryptic diversity within theD. cupreacomplex is consistent with other common and geographically widespread annelid andDiopatraspecies that are now being revealed using high-throughput sequencing.