Lonicerae japonicae flos (called Jinyinhua, JYH in Chinese), flowers or flower buds of Lonicera japonica Thunberg, is an extremely used traditional edible-medicinal herb. Pharmacological studies have already proved JYH ideal clinical therapeutic effects on inflammation and infectious diseases and prominent effects on multiple targets in vitro and in vivo, such as pro-inflammatory protein inducible nitric oxide synthase, toll-like receptor 4, interleukin-1 receptor. JYH and Lonicerae flos [called Shanyinhua, SYH in Chinese, flowers or flower buds of Lonicera hypoglauca Miquel, Lonicera confusa De Candolle or Lonicera macrantha (D.Don) Spreng] which belongs to the same family of JYH were once recorded as same herb in multiple versions of Chinese Pharmacopoeia (ChP). However, they were listed as two different herbs in 2005 Edition ChP, leading to endless controversy since they have close proximity on plant species, appearances and functions, together with traditional applications. In the past decades, there has no literature regarding to systematical comparison on the similarity concerning research achievements of the two herbs. This review comprehensively presents similarities and differences between JYH and SYH retrospectively, particularly proposing them the marked differences in botanies, phytochemistry and pharmacological activities which can be used as evidence of separate list of JYH and SYH. Furthermore, deficiencies on present studies have also been discussed so as to further research could use for reference.