Autonomously working small fish robots are ideal for surveys of fish resources and structural inspection in water where electric wires hinder the movement of the robot or radio signal (GPS etc) does not reach. The fish robot needs the self-position estimation to swim autonomously. Self-position estimation becomes possible by using visual information of bottom image in the sea or a water tank. The visual information is analyzed by means of digital image correlation method. In the study, self-position estimation is tried with use of real-time digital image correlation method and the use of FPGA (Field Programmable Gate Array), whose VHDL programming and control board was developed originally. This FPGA board executes both the control of a swimming fish robot and image processing at the same time. As a result, it has been confirmed that the small fish robot can measure swimming distance itself.