Five BOR gene family members were cloned from seedlings of trifoliate orange (Poncirus trifoliate (L.) Raf.) with RT-PCR and the expression patterns of these genes were analyzed with qRT-PCR（real-time quantitative PCR）under the boron deficiency.The results showed that the open reading frame (ORF) of PtrBOR1，PtrBOR2，PtrBOR3，PtrBOR4 and PtrBOR5 was 2 145,2 133,2 211,1 998 bp and 2 034 bp,respectively.The result of multiple sequence alignment of amino acid showed that PtrBOR1,PtrBOR2 and PtrBOR3 had the conserved endocytosis degradation and polar orientation residues.The phylogenetic tree classified PtrBOR proteins into two subgroups including one subgroup of PtrBOR1,PtrBOR2 and PtrBOR3 proteins and another subgroup of PtrBOR4 and PtrBOR5 proteins.The result of qRT-PCR analyses showed that PtrBOR4 was expressed mainly in leaves,while other PtrBORs were expressed mainly in roots.The expression of PtrBORs varied differently under the boron deficiency.The expression of PtrBOR1,PtrBOR2 and PtrBOR3 was upregulated in roots.The expression of PtrBOR1,PtrBOR2 and PtrBOR4 was upregulated in stems.The expression of PtrBOR1 was upregulated in leaves.The expression of PtrBOR1 and PtrBOR2 was upregulated in two types of tissues at least.