Qamsar cobalt deposit is located 26 km south of Kashan, in the middle part of Urumieh-Dokhtar magmatic arc. Exposed rock units in the area include Eocene volcanics, Qom Formation marine sediments and plutonic bodies. The intrusive bodies have quartz-diorite to granodiorite composition as well as porphyry microdiorite. Intruding bodies into the Eocene volcanics and Qom Formation units caused recrystallization and metamorphism and formed assemblages of skarn minerals such as garnet, pyroxene, epidote, tremolite and actinolite. Mineralization occurred as endo-skarn and exo-skarn in massive, vein, brecciated, open space filling and diffusion forms. Magnetite is the main ore mineral and is accompanied by cobaltite, chalcopyrite and pyrite. Fluid inclusion microthermometry studies were performed on prograde stage garnet and pyroxene and retrograde stage quartz. Microthermometry studies show homogenization temperatures from 400 to more than 600°C and from 180 to 200°C as well as salinities between 12 and 20% and between 5.8 and 11.9% wt NaCl equiv. for prograde and retrograde phases, respectively. Isotopic thermometry on pyrite-chalcopyrite pair minerals gives 241 to 528°C and that for quartz-magnetite pair minerals gives 441 to 549 °C. Sulfur and oxygen isotopic ratios offer magmatic origin which mixed with basinal fluid for this mineralization.