The present invention relates to a molecular marker for amplifying genetic variation of chlorophyll DNA, which can identify a pitch pine tree and a loblolly pine tree; and a method for identifying a pitch pine tree and a loblolly pine tree by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) technique by using the molecular marker. Chlorophyll DNA in coniferous trees with respect to paternal genetic traits can be used for early selection of a hybrid entity of a rigitaeda pine tree by crossbreeding the pitch pine tree and the loblolly pine tree.
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