Several halophilic archaea belonging to the genus Halococcus were isolated from stromatolites from Hamelin Pool, Shark Bay, Western Australia, collected during field trips in 1996 and 2002. This is the first incidence of halophilic archaea being isolated from this environment. Stromatolites are biosedimentary structures that have been formed throughout the earth's evolutionary history and have been preserved in the geological record for over 3 billion years. The stromatolites from Hamelin Pool, Western Australia, are the only known example of extant stromatolites forming in hypersaline coastal environments. Based on their 16S rRNA gene sequences and morphology, the isolates belong to the genus Halococcus. Strain 100NA1, isolated from stromatolites collected in 2002, was closely related to strain 100A6T that was isolated from the stromatolites collected in 1996, with a DNA–DNA hybridization value of 94±8 %. DNA–DNA hybridization values of strain 100A6T with Halococcus morrhuae NRC 16008 and Halococcus saccharolyticus ATCC 49257T were 17±6 and 11±7 %, respectively. The DNA G+C content of strain 100A6T was 60.5 mol% (Tm). The main polar lipid was S-DGA-1, a sulphated glycolipid that has been detected in all strains of the genus Halococcus. Whole-cell protein profiles, enzyme composition and utilization of various carbon sources were distinct from those of all previously characterized Halococcus species. The recognition of this strain as representing a novel species within the genus Halococcus is justified, and the name Halococcus hamelinensis sp. nov. is proposed. The type strain is 100A6T (=JCM 12892T=ACM 5227T).