There is no single observation or piece of evidence, rather the models we have describing the formation and evolution of galaxies and stars, which involve many different types of observations to arrive at those theories, suggest that breakdown in relative contributions to the total density that are summarised in the figure I linked to.
Briefly though, the mass in stellar black holes is a little tricky to measure, since we don't see these very well, but can be estimated via knowledge of the Initial Mass Function (IMF) of star clusters, since only the most massive stars end as stellar black holes. For supermassive black holes (those at the centres of galaxies) we can get an estimate of their masses from seeing either their dynamic effect on matter orbiting near them or through theories suggesting relationships between the black hole mass and the spectrum of the radiation emitted from the active region near the black hole.