In　order　to　more　reasonably　analyze　conservative　sites　and　conservative　regions　in　biological　sequences,　a　new　method　of　biological　sequences　comparison　with　constraints　on　element　position　is　proposed.　Based　on　theoretical　analysis　of　the　new　method　and　the　traditional　method,　it　is　shown　that　the　complexity　of　the　new　method　is　the　same　as　that　of　the　traditional　method,　but　the　total　amount　of　needed　computations　may　decrease　1/3　to　2/3.　Computing　experiments　show　that　the　needed　time　for　the　new　method　may　be　1/4　to　2/5　less　than　for　the　traditional　method,　and　that　the　result　computed　by　the　new　method　is　almost　the　same　as　that　by　the　traditional　method　if　the　two　sequences　are　comparable　and　the　constraints　are　proper.