An X-ray fluorescence analyzer includes a sample stage, a sample moving mechanism, an X-ray source, a detector detecting a fluorescent X-ray generated from the sample irradiated with a primary X-ray, an imaging device imaging the sample, a display device displaying the image on a screen, a pointing device designating a specific position on the screen for allowing an input at the specific position, an image processing device displaying a mark at the input position on the screen by the pointing device and a control device controlling the sample moving mechanism and the image processing device and, when the sample stage is moved, controlling the image processing device to display the mark on the screen with moving the mark in the same moving direction as that of the sample stage by the same moving distance.