An object of the present invention is to provide a circular single-stranded nucleic acid, and a method for preparing the same and a method for using the same. A circular single-stranded nucleic acid according to one embodiment of the present invention is a circular single-stranded nucleic acid for determining a target base on a genomic DNA, and includes a first single-stranded nucleic acid which has the target base or a complementary base thereto and is a part of one of the strands of the genomic DNA, and a second single-stranded nucleic acid which has an index sequence to serve as an index of a cell, from which the genomic DNA is derived, or a complementary sequence thereto.
