A PCR approach was used to isolate repeated U5 small nuclear RNA (snRNA) genes from the sea urchin Lytechinus variegatus. A 1.3 kb repeat, LvU5.0, and three other variants, LvU5.1-U5.3, that differ in the coding region and in the proximal sequence element (PSE) region were isolated. Southern Blot analysis indicate that the U5 snRNA genes, unlike other embryonically expressed snRNA genes (U1, U2 and U6), are not found in a simple tandem repeat, but instead, exist in several heterogeneous clusters each with a small number of genes. The U5 PSE has limited sequence similarity with the other sea urchin PSEs. However, when used in a mobility shift assay the U5 PSE forms a protein/DNA complex that is very similar to the complex formed with the U6 PSE. An RNase protection assay used to monitor the accumulation of U5 snRNA during development shows that at least two U5 variants are coordinately expressed during embryogenesis.