Since the nineteen-eighties, the depth, number, position and shape of the heat sources feeding the super-hot geothermal system of the Los Humeros caldera (Mexico) is under debate. With the aim of providing a seismic constraint of this region, we present a high resolution three-dimensional anisotropic shear wave velocity model. We used the continuous records of ambient seismic noise at 45 seismic stations deployed for more than one year. From the data, we obtained a set of about 1444 phase and 1534 group velocity dispersion curves, for Love and Rayleigh waves, respectively. By using the dispersion data, we obtained three dimensional models for shear wave velocities and radial anisotropy down to 17 km of depth. These models allowed to image three low velocity bodies at different depths: 1) a deep storage of potential molten material rising from the depth and stopping at ~11 km of depth, 2) a second storage region from 3 to 8 km of depth, related with the Los Humeros caldera collapse, and that feeds the 3) shallow low-velocity bodies between 1.3 and 2.2 km, representing the expression of the geothermal reservoir currently exploited. All these low velocity bodies are interconnected and represent part of the remnant magmatic plumbing system beneath the Los Humeros caldera. These seismic images provide insights to the deep upward pathways of fluids feeding the geothermal reservoir from the heat source(s) and its relationship with the structures controlling the hydrothermal system. •High resolution anisotropic ambient noise tomography of a super-hot geothermal field.•Joint interpretation of the Vs and radial anisotropy models.•Seismic image of the melt storage(s) that fed the Los Humeros geothermal system.