User's time and labor required for performing manipulations with respect to cells which exist in an incubation container, are reduced. To achieve the above, a cell observing apparatus includes an observation stage supporting an incubation container that houses cells, a micro imaging optical system forming, on an imaging device for micro imaging, an image of the cell in the incubation container disposed at an observing position of the observation stage, a macro imaging optical system forming, on an imaging device for macro imaging, an image of an area wider than that captured by the micro imaging optical system in the incubation container, and a controlling unit controlling an operation of a manipulation needle that manipulates the cells in the incubation container, in which the micro imaging optical system is disposed on a side facing the macro imaging optical system with the observation stage being located therebetween.