Abstract: Jatropha lines can be classified and discriminated by a method including the steps of: conducting a nucleic acid amplification reaction using a primer set including (i) adjacent forward primer and (ii) adjacent reverse primer, and (iii) LTR forward primer or LTR reverse primer, or (iv) RTP forward primer or RTP reverse primer, wherein DNA prepared from Jatropha that is an objective of determination, is used as a template; and determining the presence or absence of insertion of LTR-type retrotransposon including the retrotransposon sequence used in (iii) or (iv), on the basis of the presence or absence and length of an amplification product obtained by the amplification reaction.