Until recently, ammonia oxidation, a key process in the global nitrogen cycle, was thought to be mediated exclusively by a few bacterial groups. It has been shown now, that also Crenarchaeota are capable to perform this initial nitrification step. The abundance of ammonia oxidizing Bacteria and Archaea was determined using the bacterial and archaeal ammonia monooxygenase-alpha subunit (amoA) gene as functional markers in a quantitative PCR approach and related to the abundance of Bacteria and Archaea in the Eastern Mediterranean Sea. Archaeal amoA copy numbers decreased from 4000-5000 copies ml(-1) seawater from the 200-500 m depth layer to 20 copies ml(-1) at 1000 m depth. Beta-proteobacterial amoA genes were below the detection limit in all the samples. The archaeal amoA copy numbers were correlated with NO(2)(-) concentrations, suggesting that ammonia-oxidizing Archaea may play a significant role in the nitrification in the mesopelagic waters of the Eastern Mediterranean Sea. In the bathypelagic waters, however, archaeal amoA gene abundance was rather low although Crenarchaeota were abundant, indicating that Crenarchaeota might largely lack the amoA gene in these deep waters. Terminal restriction fragment length polymorphism analysis of the archaeal community revealed a distinct clustering with the mesopelagic community distinctly different from the archaeal communities of both, the surface waters and the 3000-4000 m layers. Hence, the archaeal community in the Eastern Mediterranean Sea appears to be highly stratified despite the absence of major temperature and density gradients between the meso- and bathypelagic waters of the Mediterranean Sea.