Vortex patterns at very low vortex densities in high quality MgB2 single crystals are studied by scanning SQUID microscopy. In observations, characteristically vortices tend to line up locally at very low vortex densities and then form vortex cluster structure with increasing applied field. The evolution of vortex clusters is elucidated by molecular dynamics (MD) simulations based on a two-gap Ginzburg–Landau (GL) theory with type-1.5 conditions. In both observations and simulations, the average intervortex distance in clusters is independent of the applied field. The agreement confirms that high quality MgB2 single crystals lie in the type-1.5 regime.