Abstract As counterions of DNA on mica, Mg 2+, Ca 2+, Sr 2+ and Ba 2+ were used for clarifying whether DNA molecules equilibrate or are trapped on mica surface. End to end distance and contour lengths were determined from statistical analysis of AFM data. It was revealed that DNA molecules can equilibrate on mica when Mg 2+, Ca 2+ and Sr 2+ are counterions. When Ba 2+ is present, significantly crossovered DNA molecules indicate that it is most difficult for DNA to equilibrate on mica and the trapping degree is different under different preparation conditions. In the presence of ethanol, using AFM we have also observed the dependence of B–A conformational transition on counterion identities. The four alkaline earth metal ions cause the B–A transition in different degrees, in which Sr 2+ induces the greatest structural transition.