The use of phylogenetic methods in linguistics has provided new insights into the structure, age, and spread of language families. Despite increasing recognition of Japonic as one of the world’s primary language families, research on the family’s phylogeny remains limited. This study presents a new reconstruction of Japonic language history based on NichiRyuuLex, a new lexical dataset comprising data from 48 Japanese and 33 Ryukyuan lects for 256 concepts. The study takes a novel approach, combining lexical and phonotactic data to increase precision in the phylogenetic parameter estimates, providing a more informative reconstruction. The analyses presented here confirm previous findings on the age of the family as a whole, estimating a Japanese-Ryukyuan split at around 500 BCE, supporting that the time of diversification coincides with the influx of Bronze Age rice agriculturists during the Yayoi Period. The topology of the mainland Japanese clade uncovered in the analyses unifies two divisions recognised in traditional Japanese dialectology (the East-West division, and the center-periphery division). The topology of the Ryukyuan clade largely followed geographical segmentation—Northern Ryukyuan (Amami; Okinawa) vs. Southern Ryukyuan (Miyako; Macro-Yaeyama). The ancestor of Ryukyuan was dated to around the 9th century, coinciding with the first traces of cereal farming in the Northern Ryukyu Islands. In sum, the study provides greater certainty about the linguistic history and internal structure of mainland Japanese, as well as a more detailed perspective on the history of the Ryukyuan languages.