An apple ESTs local database of apple fruit (Malus domestica CV red Fuji) was constructed by differential screening and a large number of sequencing against the suppression subtractive hybridization cDNA library from M. domestica Cultivar red Fuji coloring type sports and its wild type. A metallothionein (MT) gene, named MdFjMT2 (Accession No. HQ730757) was cloned by RT-PCR and splicing of 42 cDNA sequences that were obtained by Blastn searching against the ESTs local database. The full length cDNA encoding metallothionein gene MdFjMT2 was 686 bp, including 97 bp of 5′ untranslated region and 319 bp of 3′ untranslated region. It had an open reading frame (ORF) of 240 bp, encoding 79 amino acid residues. The protein molecular weight was 7.7938 kD and theoretical pI was 4.75. The MdFjMT2 contained the conserved domains of all known MT, with 14 Cys (C) residues, ranking in the feature of CC, CXC and CXXC, and locating at protein N terminal and C terminal. The phylogenetic tree analysis revealed that amino acids sequence of MdFjMT2 shared the higher similarity with Pyrus pyrifolia, M. domestica and M. xiaojinensis but the lower similarity with Prunus dulcis, Salix matsudana and Actinidia deliciosa. Bioinformatics analysis showed that MdFjMT2 mainly located in chloroplasts, it had no signal peptide and belonged to the hydrophilic non-transmembrane protein, it had no functional domains and random coil was the major components of its secondary structure. These results provided some information for the further structure and function study of MdFjMT2. The results would be useful to study the gene's functions, and clarify molecular mechanisms of apple coloring.