We analyse the CO-dark molecular gas content of simulated molecular clouds from the SILCC-Zoom project. The simulations reach a resolution of 0.1 pc and include H 2 and CO formation, radiative stellar feedback and magnetic fields. CO-dark gas is found in regions with local visual extinctions A V,3D ∼ 0.2 -1.5, number densities of 3 -300 cm −3 and gas temperatures of few 10 K -100 K. CO-bright gas is found at number densities above 300 cm −3 and temperatures below 50 K. The CO-dark gas fractions range from 40% to 95% and scale inversely with the amount of well-shielded gas (A V,3D 1.5), which is smaller in magnetised molecular clouds. We show that the density, chemical abundances and A V,3D along a given line-of-sight cannot be properly determined from projected quantities. As an example, we show that pixels with a projected visual extinction of A V,2D ≃ 2.5 -5 can be both, CO-bright and CO-dark. By producing synthetic CO(1-0) emission maps of the simulations with RADMC-3D, we show that about 15 -65% of the H 2 is in regions with CO(1-0) emission below the detection limit. The simulated clouds have X CO -factors around 1.5 × 10 20 cm −2 (K km s −1 ) −1 with a spread of up to a factor ∼ 4, implying a similar uncertainty in the derived total H 2 masses and even worse results for individual pixels. Based on our results, we suggest a new approach to determine the H 2 mass, which relies on the availability of CO(1-0) emission and A V,2D maps. It reduces the uncertainty of the clouds' overall H 2 mass to a factor of 1.8 and for individual pixels, i.e. on sub-pc scales, to a factor of 3.