Nucleotide sequences of the second intron of the nuclear LEAFY gene (FLint2) and trnL-trnF region of the chloroplast genome were used to analyze the phylogenetic relationships among eight wild mandarins (Citrus reticulata Blanco), 19 mandarin landraces, and 19 related species of Citrus L. Forty-six trnL-trnF sequences and 111 FLint2 sequences were obtained from 46 ingroup accessions, with an average length of 1059.7 and 776.7 bp respectively. Phylogeny reconstructions were conducted separately for these two data sets using maximum parsimony and maximum likelihood criteria. Monophyly of mandarins was supported by both of these data sets, and in this clade, most mandarin landraces formed an unresolved polytomy, whereas ‘Jiangyong 1’, ‘Chongyi A2’, ‘Chongyi A1’ (or ‘Jiangyong 4’ in FLint2 data), and ‘Daoxian 1’ wild mandarins formed a subclade. ‘Mangshan A1’ and ‘Daoxian 5’ wild mandarins were sisters to this mandarin clade. A hybrid origin of five mandarin landraces and several mandarin-related species was suggested as a plausible hypothesis to explain the incongruence between the FLint2 and trnL-trnF data sets.