With the altitude of 3570 m, this is so far the highest site where actively forming non-lithified stromatolites have been found, located at the shore of a volcanic, alkaline lake Socompa (Argentina). To assess the variation of the microbial community composition along the physico-chemical gradients characterizing the uppermost seven millimeters of these structures, we employed 454 pyrosequencing in the top six visible laminations (layers). Given the relatively good characterization of the physico-chemical gradients in the top few millimeters of the stromatolite, the aim of this study were to evaluate how the local diversity and composition of the microbial community varies along these gradients, and which traits they share with other modern stromatolites reported.