An outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurred aboard the Diamond Princess cruise ship between her January 20 departure and late February 2020 . Here, we used phylodynamic analyses to investigate the transmission dynamics of SARS-CoV-2 during the outbreak . Using a Bayesian coalescent-based method, the estimated mean nucleotide substitution rate of 240 SARS-CoV-2 whole-genome sequences was approximately 7.13 × 10−4 substitutions per site per year . Population dynamics and the effective reproductive number (Re) of SARS-CoV-2 infections were estimated using a Bayesian framework . The estimated origin of the outbreak was January 21 , 2020 . The infection spread substantially before quarantine on February 5 . The Re peaked at 6.06 on February 4 and gradually declined to 1.51, suggesting that transmission continued slowly even after quarantine . These findings highlight the high transmissibility of SARS-CoV-2 and the need for effective measures to control outbreaks in confined settings.