Supplementary Data for the under-reviewing article "Phylogenetic evidence reveals early Kra-Dai divergence and dispersal in the late Holocene". Supplementary Data 1: The lexical cognate database of Kra-Dai languages. Sheet 1 “Lexical items” shows the language entries and lexical items of 100 Kra-Dai languages. Sheet 2 “Binary coded sets” shows the binary coded form based on Sheet 1. Sheet 3 “Note” shows the reason for deleting specific lexical items and descriptions for the data. Supplementary Data 2: Node constraints with known historical information used to calibrate the divergence time calculations in BEAST. Supplementary Data 3: Model comparison among different combinations of models in BEAST. Sheet 1 “HME” shows the results compared by Harmonic Mean Estimator. Sheet 2 “Path Sampling” shows the results compared by the path sampling method. Supplementary Data 4: Possibilities of ancestral area. Supplementary Data 5: Comparison of time depth and root probability among versions of different settings. Supplementary Data 6: Delta score and Q-residual. Supplementary Data 7: Information on archaeological sites in South China and MSEA. Supplementary Data 8: Resources of linguistic data. Supplementary Data 9: BEAST xml files, nexus files, MCC tree file, and log file. Supplementary Data 10: Statistical significance among models of dispersal routes in the posterior samples of 3 independent runs of the RJMCMC. Supplementary Data 11: The control file, input file, and geographical distribution file used in the BayesTraits program. 3 MCMC run log files were also included. Supplementary Data 12: Kra-Dai population samples used for BSP analysis. Supplementary Data 13: The interdisciplinary data and code used to plot Figure 3.