In the effort to understand the link between the structure of galaxy clusters and their galaxy populations, we focus on MACSJ1206.2-0847 at z~0.44 and probe its substructure in the projected phase space through the spectrophotometric properties of a large number of galaxies from the CLASH-VLT survey. Our analysis is mainly based on an extensive spectroscopic dataset of 445 member galaxies, mostly acquired with VIMOS@VLT as part of our ESO Large Programme, sampling the cluster out to a radius ~2R200 (4 Mpc). We classify 412 galaxies as passive, with strong Hdelta absorption (red and blue galaxies, and with emission lines from weak to very strong. A number of tests for substructure detection are applied to analyze the galaxy distribution in the velocity space, in 2D space, and in 3D projected phase-space. Studied in its entirety, the cluster appears as a large-scale relaxed system with a few secondary, minor overdensities in 2D distribution. We detect no velocity gradients or evidence of deviations in local mean velocities. The main feature is the WNW-ESE elongation. The analysis of galaxy populations per spectral class highlights a more complex scenario. The passive galaxies and red strong Hdelta galaxies trace the cluster center and the WNW-ESE elongated structure. The red strong Hdelta galaxies also mark a secondary, dense peak ~2 Mpc at ESE. The emission line galaxies cluster in several loose structures, mostly outside R200. The observational scenario agrees with MACS J1206.2-0847 having WNW-ESE as the direction of the main cluster accretion, traced by passive galaxies and red strong Hdelta galaxies. The red strong Hdelta galaxies, interpreted as poststarburst galaxies, date a likely important event 1-2 Gyr before the epoch of observation. The emission line galaxies trace a secondary, ongoing infall where groups are accreted along several directions.
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