:The siphonous green alga Codium fragile currently has 10 accepted subspecies, among which is the problematic invasive subsp. fragile. The subspecies are defined on the basis of five polymorphic nucleotides in the plastid rps3–rpl16 spacer region, and this subdivision into subspecies has not been investigated in detail with other DNA markers. Here, we compiled a data set of the green algal DNA barcoding marker tufA that includes 110 C. fragile specimens and an additional 80 specimens of eight related Codium species. Our tufA haplotype tree showed two distinct clades within C. fragile, and the three algorithmic species delimitation methods that were applied agreed that these are likely to represent separate species. The first clade consisted of the invasive subspecies fragile, whereas the second contained the remaining subspecies present among our sequences. Using a newly developed morphometric method to capture fine details of utricle morphology, we show that the two molecular clades also have subtle morphological differences. Despite all this new evidence in favour of two species being present in C. fragile, we refrain from making formal taxonomic changes, chiefly because our tufA data do not agree with previous rps3–rpl16 results. We propose four complementary approaches to resolve these conflicts.