We have developed an in-air particle-induced x-ray emission(PIXE) analysis system that provides elemental distribution images in a region of 3 × 3 cm2 with a spatial resolution of ∼0.5 mm. We call this system an in-air submilli-PIXE camera. This system consists of a submilli-beam line, beam scanners and a data acquisition system for elemental mapping. We applied the in-air submilli-PIXE camera to phytoremediation research. Phytoremediation is a technology for cleaning metal-contaminated soils using plant physiology. Pteris vittata, which is known as a hyperaccumulator of arsenic, was analyzed by the PIXE camera. Elemental images of laminas were obtained in vivo without sample preparation. The elemental map of the laminas in several centimeters region showed that arsenic was accumulated in the edges of P. vittata fronds and redistributed in the laminas at different growth stages. The submilli-PIXE camera is an effective tool for undertaking phytoremediation research.