Waterlilies (Nymphaea) play an increasingly important role in water garden, water purification and ecological construction. This paper reviews the advances on studies of germplasm resources, breeding objectives, breeding techniques and achievements. (1) The genetic diversity of waterlilies in China is constitutively increasing. Only five species were originally found in China, which accounted for only 10% of global water lily species. Nowadays, over 30 exotic species and 400 cultivars have been conserved, in which the flowering biology has been studied. (2) The modern breeding aimed at the selection of colorful cultivars before 2009, while breeding for hardy waterlilies with blue-purple flower colors by inter-subgenera crosses has been thereafter conducted. However, this international breeding steps of waterlilies didn’t meet to the demand in domestic market. (3) Application of advanced breeding methods. The cross combinations have moved from intraspecific, interspecific to inter-subgeneric. The hybridizing technology without emasculation of waterlily has been invented and the efficiency of hybridization has been improved. The inheritance of some characteristics in waterlilies was analyzed. Some new techniques such as physical and chemical mutagenesis, ploidy breeding and transgenic breeding have been applied to the breeding of waterlilies. (4) Over past 20 years, Chinese breeders have released 205 new varieties including 18 nationally-approved cultivars and 187 internationally-registered cultivars. Especially, these four varieties, composing of ‘Hong Yanyan’, ‘Lan Jian’, 'Tian Ci' and 'Detective Erika', have been approved by winning six awards in the International New Waterlily Competition.