The occurrence and origin of methane (CH4) generated by serpentinization of ultramafic rocks is of current timely interest in planetary geology, astrobiology and energy resource exploration, as it may contribute, in particular, to decipher the source of methane on Mars, the origin of life and the potential of abiotic hydrocarbon synthesis. Methane of dominant abiotic origin in serpentinized peridotites on continents (ophiolites or igneous intrusions) has been documented so far, with complete carbon and hydrogen isotope composition, in six countries, in the Philippines, Turkey, Oman, New Zealand, Japan and Italy. We report the discovery of two new sites in Greece, at Archani and Ekkara, located in the Othrys ophiolite massif. Portable sensors based on Fourier Transform InfraRed spectrometry (FTIR) and Tunable Diode Laser Absorption Spectroscopy (TDLAS) allowed to realize that out of 21 ophiolitic springs, methane is released only by four hyperalkaline (pH from 10.7 to 11.3) and calcium hydroxide (Ca–OH) type waters; all other 17 springs with pH < 8.7 and magnesium-rich waters in the Pindos, Vourinos and Veria ophiolites, do not show methane. This correlation between gas occurrence and water type seems to occur worldwide; accordingly, CH4 production appears to be intimately related to the depth and residence time of the circulating meteoric waters. Methane is emitted into the atmosphere also from the soil surrounding the hyperalkaline springs, with fluxes of the same order of magnitude (~ 102–103 mg m− 2 day− 1) of seepage typically observed over conventional petroleum systems. Othrys CH4 has an isotopic composition (δ13C from − 27‰ to − 37.3‰ VPDB, δ2H from − 250‰ to − 311‰ VSMOW) similar to that reported in ultramafic rocks in New Zealand and Japan, and in Precambrian crystalline shields, which were considered dominantly abiotic and probably derived from Fischer–Tropsch Type reactions. The paucity of CO2, which is the norm in hyperalkaline waters, and of other hydrocarbons prevents from evaluating possible mixing of gas of different sources, including microbial methanogenesis. Also the H2 content is trivial, notwithstanding it being a typical product of serpentinization; this could be due to complete H2 consumption by CO2 reduction in a limited or decreased H2 production system due, for example, to a late stage of increased silica activity, as suggested by preliminary petrographic observations. The low geothermal gradient of the area and the present-day serpentinization imply that, whatever the CH4 production mechanism, it took place at temperatures below those traditionally considered for the origin of abiotic methane in hydrothermal systems.