Biominerals can achieve complex shapes as aggregates of crystalline building blocks. In the red coral skeleton, we observe that these building blocks are arranged into eight hierarchical levels of similarly (but not identically) oriented modules. The modules in each hierarchical level assemble into larger units that comprise the next higher level of the hierarchy, and consist themselves of smaller, oriented modules. EBSD and TEM studies show that the degree of crystallographic misorientation between the building blocks decreases with decreasing module size. We observe this organization down to a few nanometers. Thus, the transition from imperfect crystallographic order at millimeter scale to nearly perfect single crystalline domains at nanometer scale is progressive. The concept of “mesocrystal” involves the three-dimensional crystallographic organization of nanoparticles into a highly ordered mesostructure. We add to this concept the notion of “multilevel modularity.” This modularity has potential implications for the origin of complex biomineral shapes in nature. A multilevel modular organization with small intermodular misorientations combines a simple construction scheme, ruled by crystallographic laws, with the possibility of complex shapes. If the observations we have made on red coral extend to other biominerals, long-range crystallographic order and interfaces at all scales may be key to how some biominerals achieve complex shapes adapted to the environment in which they grow.