To obtain desired images by properly controlling units even when the units are changed.

An image acquisition system includes a mutually communicatable server 3 through a network 4 and an image acquisition device 2. The image acquisition device 2 includes a plurality of the units 5, 6, 8, 9, 10, 11, 12, 13, 22 for acquiring images of an observation object (A) and a control device 30 for controlling the units by storing a control software. The server 3 includes a storage part 35 for storing to correlate pieces of unit information 33a-33f for discriminating the units and the pieces of control software 34a, 34b in response to the pieces of unit information 33a-33f. The image acquisition device 2 transmits the unit information of the unit to the server 3. In the image acquisition system 1, the server 3 transmits the pieces of control software 34a, 34b stored to be correlated to transmitted unit information to the image acquisition device 2.