We aim at constraining evolutionary models at low mass and young ages by identifying interesting transiting system members of the nearest OB association to the Sun, Upper Scorpius, targeted by the Kepler mission. We produced light curves for M dwarf members of the USco region surveyed during the second campaign of the Kepler K2 mission. We identified by eye a transiting system, UScoJ161630.68-251220.1 (=EPIC203710387) with a combined spectral type of M5.25 whose photometric, astrometric, and spectroscopic properties makes it a member of USco. We conducted an extensive photometric and spectroscopic follow-up of this transiting system with a suite of telescopes and instruments to characterise the properties of each component of the system. We calculated a transit duration of about 2.42 hours occuring every 2.88 days with a slight difference in transit depth and phase between the two components. We estimated a mass ratio of 0.922+/-0.015 from the semi-amplitudes of the radial velocity curves for each component. We derived masses of 0.091+/-0.005 Msun and 0.084+/-0.004 Msun,radii of 0.388+/-0.008 Rsun and 0.380+/-0.008 Rsun, luminosities of log(L/Lsun)=-2.020 (-0.121+0.099) dex and -2.032 (-0.121+0.099) dex, and effective temperatures of 2901 (-172+199) K and 2908 (-172+199) K for the primary and secondary, respectively. We present a complete photometric and radial velocity characterisation of the least massive double-line eclipsing binary system in the young USco association with two components close to the stellar/substellar limit. This system fills in a gap between the least massive eclipsing binaries in the low-mass and substellar regimes at young ages and represents an important addition to constrain evolutionary models at young ages.
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