The green algal genus Cloniophora has been classified in the Chaetophorales (Chlorophyceae) based on morphological characters. This study uses DNA sequence data from the nucleus (SSU) and the chloroplast (tufA) from collections in the Hawaiian Islands and a culture originating from Portugal to test this classification. Taxonomic identities of contemporary collections were confirmed by sequencing small fragments of DNA (rbcL and SSU) from type specimens, including the generitype, Cloniophora willei L. H. Tiffany. These molecular data show that Cloniophora does not have close affinities to the Chaetophorales and belongs instead to the Ulvales (Ulvophyceae). The morphological features of eight or more reproductive products per cell and a pyrenoid with a traversing thylakoid membrane support the molecular data and confirm the placement of this group in the Ulvales. As this genus does not belong to any recognized family in the Ulvales, the family Cloniophoraceae, containing the single genus Cloniophora, is proposed.