Mn-doped CdSe nanocrystals encapsulated in carbon (Cd1-xMn xSe @ C) were synthesized by the one-pot RAPET (reaction under autogenic pressure at elevated temperature) approach. The nanocrystal core was 27-51 nm encapsulated by a 9-18 nm carbon shell, as evidenced from electron microscopic analysis. The efficient replacement of Cd by Mn in the hexagonal wurtzite Cd1-xMnxSe lattice, until Mn/Cd = 0.099, was confirmed from electron paramagnetic resonance (EPR) experiments. For Mn/Cd = 0.143 nanocrystals, manganese was found to be expelled to the nanocrystal surface. The magnetic measurements evidenced the appearance of antiferromagnetic clusters (manganese rich) that exhibit a superparamagnetic behavior with a blocking temperature of 28 K. Raman experiments revealed that me shell consisted of continuous linear chains of carbon. The formation of the core-shell nanocrystals in the absence of any templating agent was a kinetically controlled process of Cd1-xMnxSe nucleus formation and carbon encapsulation. Mn replaces Cd mainly in the (100) plane and catalyzes the formation of nanorods and tripod nanostructures.