An endoscope system, comprising: an acquisition unit (61, 62) that acquires a first still image and automatically acquires a video before and after acquisition of the first still image based on an image signal obtained by imaging an observation target using an image sensor; an association unit that associates the first still image with the video; a storage unit that stores the first still image and the video associated with each other; an imaging optical system capable of changing an imaging magnification of the observation target; an imaging magnification change operation unit for inputting an imaging magnification change instruction to change the imaging magnification to the imaging optical system; and wherein a first mode and a second mode different from the first mode are prepared as modes for acquiring the first still image and the video, wherein one of the first and second mode is a normal observation mode in which the observation target is observed using normal light and the other of the first and second mode is a special observation mode in which the observation target is observed using special light, a control unit that performs control to acquire the first still image by one of the first and second modes based on the imaging magnification change instruction and then start by switching the one mode to the other mode acquisition of the video, a focus detection unit that detects a focus of an image to be acquired, wherein the control unit performs control to end the acquisition of the video when both the focus detection unit detects that the image is in focus after acquisition of the first still image and an operation end of the imaging magnification change operation unit is detected. an acquisition unit (61, 62) that acquires a first still image and automatically acquires a video before and after acquisition of the first still image based on an image signal obtained by imaging an observation target using an image sensor; an association unit that associates the first still image with the video; a storage unit that stores the first still image and the video associated with each other; an imaging optical system capable of changing an imaging magnification of the observation target; an imaging magnification change operation unit for inputting an imaging magnification change instruction to change the imaging magnification to the imaging optical system; and wherein a first mode and a second mode different from the first mode are prepared as modes for acquiring the first still image and the video, wherein one of the first and second mode is a normal observation mode in which the observation target is observed using normal light and the other of the first and second mode is a special observation mode in which the observation target is observed using special light, a control unit that performs control to acquire the first still image by one of the first and second modes based on the imaging magnification change instruction and then start by switching the one mode to the other mode acquisition of the video, a focus detection unit that detects a focus of an image to be acquired, wherein the control unit performs control to end the acquisition of the video when both the focus detection unit detects that the image is in focus after acquisition of the first still image and an operation end of the imaging magnification change operation unit is detected.