The Anammox process, involving transformation of ammonium to dinitrogen, is well known in aquatic ecosystems. However, this anaerobic process in soil has been little explored, even less in extremophile soils. The saline-sodic soil of the former Lake Texcoco exposed to desertification with irrigation projects using wastewater of Mexico City, is a unique environment, yet little is known about its microbial ecology. The objective of this study was to examine the presence of Anammox microorganisms and their microcosm activity after a period of Anammox enrichment (229 days). Microcosm kinetics monitored after the 229 days enrichment experiment, showed a significant removal of ammonium and nitrite, with a significant production of dinitrogen. The stoichiometric conversion of NO2– and NH4+ to N2 gas is complete in the studied soils, based on an Anammox process where 1 mole of NH4+ resulted in 1.02 moles of N2. The presence of the Anammox functional gene hzoA was observed in saline-sodic soils of the former Lake Texcoco. The Anamx1 and Anamx2 operational taxonomic units (OTU) are phylogenetically close to a bacterium of the phylum Planctomycetes from a wastewater treatment reactor and marine environment (AB257585.1 and HE654780.1, respectively). Those two OTU represent indigenous or exogenous Anammox microorganisms phylotypes. The existence of microorganisms with Anammox activity in a saline-sodic alkaline soil is of great interest for the understanding of the nitrogen cycle in extremophile soils.