The main plank of evidence is from the estimated primordial abundances of helium, deuterium and lithium. Big bang nucleosynthesis predicts what these primordial abundances should be as a function of the baryon to photon ratio in the early universe.
In turn, this baryon to photon ratio leads to an estimate of the ratio of the baryon density to the critical density of the universe multiplied by the present-day Hubble parameter (squared) $\Omega_b h^2$.
Now we know from looking at the dynamics of galaxies; from the dynamics of galaxies in clusters and from a careful analysis of the fluctuations of temperature in the cosmic microwave background that the ratio of "matter" density to the critical density is $\sim 0.3$ (see for example Ade et al. 2015). On the other hand, we know from the primordial abundance estimates that $\Omega_b h^2 \sim 0.02$ (e.g. see here). Given that we know the present day Hubble parameter to be $h \sim 0.7$, this indicates that only 4 per cent of the critical density is in the form of baryonic matter and thus that 26 percent of the critical density is "matter" in a form which is non-baryonic.
Given that neutrinos and electrons (i.e. leptons) can easily be shown to have a negligible contribution, then we conclude that the majority (about 80 per cent) of matter in the universe is non-baryonic and of a form that does not interact electromagnetically (a.k.a. dark matter).
A second piece of evidence comes from attempts to model how the structures that we see in the present-day universe have evolved from the structures implied by the non-uniformities in the cosmic microwave background. A summary would be that it is impossible to have the rapid evolution of structure that is seen from the tiny fluctuations in the CMB, unless those structures had already been seeded by gravitating matter that was able to "decouple" from the ordinary (baryonic) matter and radiation at earlier epochs. This role is played by non-baryonic dark matter.