Chaetomorpha melagonium is a morphologically distinct species of green algae that occurs throughout the North Atlantic, the North Pacific and the Arctic Ocean. In this study, we analyzed the intraspecific genetic diversity among 14 samples of C. melagonium from across the distribution range based on nuclear large subunit ribosomal DNA (LSU rDNA) and rDNA internal transcribed spacer (ITS) DNA sequences. All samples had identical LSU sequences. The ITS sequences had very few mutations that nevertheless divided the specimens into two groups: one included samples from Iceland, Svalbard, Massachusetts and Alaska with identical ITS sequences; members of this group differed in samples from Europe (France, Germany, Scotland, Sweden, and Wales) by three mutations (two point mutations and one five base pair indel). The European specimens had identical ITS sequences with the exception of a single sample from Brittany that differed by one base pair. The maximum ITS sequence divergence within the samples of C. melagonium was less than 0.5%. This low intraspecific variation in the frequently used highly variable ITS region is discussed in the context of past geological and climatic scenarios.