Low copy nuclear genes show great potential to provide phylogenetic information, but their use has been hampered by several inherent adverse factors. Polymerase chain reaction (PCR)-mediated recombination ranks among these factors and occurs when high levels of similar paralogs for a low-copy nuclear gene coexist within a single PCR amplification reaction. In this study, the LEAFY gene was cloned and sequenced for 63 Cinnamomum species and two copies of the second intron were found within species of the diploid sect. Cinnamomum. Although these two copies are very similar, they can be distinguished easily due to a specific ca. 47-bp segment that is missing in the “short sequence” copy. The “long sequence” copy performed well in phylogenetic analysis of Cinnamomum and is largely consistent with phylogenetic relationships based on internal transcribed spacer region sequences. In contrast, the “short sequence” copy was problematic for phylogenetic reconstruction and PCR-mediated recombination was detected in 20 of the 38 Cinnamomum species with two LEAFY copies. Thirty-one recombinants were discriminated and the breakpoints suggested by the programs RDP3 and GARD were distributed randomly along the recombination sequences. This study shows that duplication in low-copy nuclear genes and problems associated with PCR-mediated recombination need to be given more attention in phylogenetic studies.