Ultra-deep observations of ECDF-S with Chandra and XMM-Newton enable a search for extended X-ray emission down to an unprecedented flux of $2times10^{-16}$ ergs s$^{-1}$ cm$^{-2}$. We present the search for the extended emission on spatial scales of 32$^{primeprime}$ in both Chandra and XMM data, covering 0.3 square degrees and model the extended emission on scales of arcminutes. We present a catalog of 46 spectroscopically identified groups, reaching a redshift of 1.6. We show that the statistical properties of ECDF-S, such as logN-logS and X-ray luminosity function are broadly consistent with LCDM, with the exception that dn/dz/d$Omega$ test reveals that a redshift range of $0.2<z<0.5$ in ECDF-S is sparsely populated. The lack of nearby structure, however, makes studies of high-redshift groups particularly easier both in X-rays and lensing, due to a lower level of clustered foreground. We present one and two point statistics of the galaxy groups as well as weak-lensing analysis to show that the detected low-luminosity systems are indeed low-mass systems. We verify the applicability of the scaling relations between the X-ray luminosity and the total mass of the group, derived for the COSMOS survey to lower masses and higher redshifts probed by ECDF-S by means of stacked weak lensing and clustering analysis, constraining any possible departures to be within 30% in mass. Abridged.
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