There are two known ludwigites containing a single transition metal element, Fe3O2BO3 and Co3O2BO3. The structure of these materials has low-dimensional units in the form of three-legged ladders (3LL) that confer to each of them unique magnetic and electronic properties. Fe3O2BO3 presents a staggered charge density wave (CDW) transition in the ladders near room temperature and two magnetic transitions. It has remained a mystery why the other compound Co3O2BO3 behaves so conventionally, with a single magnetic transition and no CDW in spite of similar structural and electronic configurations. Neutron diffraction results presented here in this system finally unravel these differences. Far from a trivial explanation, we uncover a coexistence of low and high spin Co ions in well-defined octahedral sites. Our results allow one to solve the contrasting behavior of the Fe and Co ludwigites in terms of a subtle and unique charge ordering mechanism occurring at the microscopic level of the rungs of the 3LL.