The present invention relates to a technique for efficient isolation of long nucleic acids and short nucleic acids from a sample containing long nucleic acids and short nucleic acids via safe and convenient operations. Specifically, long nucleic acids and short nucleic acids are isolated from a sample containing nucleic acids by mixing a chaotropic agent with the sample containing nucleic acids, allowing the mixed solution to pass at least twice through a first solid phase containing silica that has passage pores having predetermined pore sizes, allowing the mixed solution to pass at least twice through a second solid phase containing silica that has passage pores having pore sizes smaller than those of the first solid phase containing silica, and separately recovering nucleic acids that have bound to the first solid phase containing silica and those that have bound to the second solid phases containing silica.