A target substance capturing device includes a supporting member to place and support a metal-film coated structure that captures a target substance, and including at least two holes opening at portions different from a portion where the metal-film coated structure is placed, a holding member that puts the metal-film coated structure in between the holding member and the supporting member, and including an opening portion that overlaps with the holes of the supporting member, and a portion that captures the target substance in the metal-film coated structure placed on the supporting member, and a covering member having transparency, and covering the opening portion of the holding member.