Abstract: In order to tackle the challenges brought by the changing environment, the hydrological gene theory is established to explore the evolution rules of water resources of Southwest rivers in this article. The hydrological genes are based on different moments that reflect the heredity and variability characteristics of hydrological variables. A hydrological gene detection system with the functions of identification and significance gradation is developed first based on the correlation principle. Then, the hydrological gene detection system is applied to the annual runoff time series of six secondary water resources regions in Southwest rivers basin (SWRSRB). The hydrologic gene components based on the first-, second- and third-moment are extracted, including nonstationary components (jump, local- and global-trend, periodicity, and dependence) and genetic components (randomness). After that, the concept of hydrological gene map and the method for drawing it are proposed to demonstrate the hydrological gene information. The results show that there are different kinds of hydrological gene variation components in the first-order moment series, mainly manifesting in the form of jump, local trend, periodicity, and dependence. The second-order moment series of the Nujiang River and Irrawaddy River basin only contain the genetic component, while the rest second-order moment series have weak periodicities. Compared with the first- and second-order moment series, the hydrological gene composition of the third-order moment series is relatively simple, with a weak influence on the original series. Attribution analysis shows that the first-order moment series of water resources evolution in SWRSRB are mainly controlled by precipitation.