Focusing on the dominant stresses of rice production in Southern China, we have carried out germplasm evaluation and innovation in rice for more than 10 years. A set of genes have been cloned or sequence-optimized, including the drought tolerance genes AtDREB1A and CbDREB1A, the herbicide resistance genes Epsps#, Pat# and Mat#, the lepidopteran resistance genes Cry2Aa# and Cry1Ca#, and the phytase-lactoferricin fusion gene PhyLf. The innovated rice germplasm covered Bar68, a glufosinate resistance indica rice variety for early cropping season; EB7001S, a male sterile line with both glufosinate and glyphosate resistance; BPL9K, a glufosinate resistance rice variety as well as with both phytase and antibacterial activity in grains; B2A4008S, B2A68, B1C893 and B1C106, the rice varieties with both glufosinate resistance and lepidopteran resistance; and some glufosinate resistance rice varieties with drought tolerance, or with salinity tolerance, or with cold tolerance. Some rice germplasm with better thermal tolerance or drought tolerance were selected out from javanica rice resource, or from indica/javanica recombinant inbred lines, or from japonica rice resource. Some key parental lines of hybrid rice, including Huazhan, Yuehui9113, Y58S, and Guangzhan63S etc., were improved in both brown planthopper resistance and bacterial blight resistance. A submergence tolerance line Sub-1BS was developed by marker-assisted selection and twice submergence stress method. The evaluated and innovated rice germplasm as described above will provide strong support for future stress tolerance breeding in rice.