This research reveals the different expression patterns of anthocyanin biosynthesis enzyme genes and transcription factors in six red-skinned pear cultivars with different genetic backgrounds. Skin color is an important feature of pear fruits, with red skin generally attracting consumers. However, great differences of coloration exist in different pear cultivars. To elucidate the characteristics of pigmentation in pear cultivars with different genetic backgrounds, six cultivars, belonging to P. communis, P. pyrifolia, P. ussuriensis, P. bretschneideri, and a hybrid of P. communis × P. pyrifolia, were used to detect pigment concentrations, expressions of seven anthocyanin biosynthesis enzyme genes, and three related transcription factor genes. Results showed that the occidental pears 'Starkrimson' and 'Red Bartlett' colored at the beginning of fruit setting, but color decreased with fruit maturity; the other four cultivars showed low anthocyanin accumulations and the contents increased during fruit development, but also decreased at later stages. The expression patterns of genes encoding enzymes indicated that ANS and UFGT were decisive genes for anthocyanin biosynthesis for red-skinned pear, and their different expressions led to the coloration differences between occidental and oriental pears. The expression patterns of transcription factors indicated that the different co-expression of MYB10 and bHLH33 genes and the different expressions of WD40 are involved in the differential regulation mechanisms of anthocyanin biosynthesis and coloration pattern between occidental and oriental pears.