Based on field investigation and documents collection, we counted endemic seed plants in Chongqing, and analyzed their floristic characteristics. The results were as follows: (1) There were 153 endemic seed plant species in Chongqing, which belong to 97 genera and 40 families. Most of them were herbaceous plants, about 103 species, followed by shrubs and trees. (2) The geographical compositions were complex and diverse. There were 6 distribution types and 1 subtype for families, 8 types and 10 subtypes for genera. According to ecological function regionalization of Chongqing, the endemisms were divided into 11 types. (3) At the level of family, tropicsubtropic elements occupied 57.14%, whereas temperate elements occupied 42.86%. At the level of genus, tropicsubtropic elements occupied 23.53%, whereas temperate elements occupied 64.71%. Transitional characteristic is obvious. (4) The distribution centersis obvious and the abundance order was: Jinfo Mountain evergreen broadleaf forest biodiversity conservation ecofunction region>Daba Mountain biodiversity conservation and water and soil conservation ecofunction region>outskirts headwaters>hydrofluctuation belt constructed wetlands.