We illustrated our method with a reconstruction of a plausible scenario for the spatiotemporal spread of the A/H1N1 influenza strain during the early stages of the 2009 influenza pandemic. This data set might not be ideal for showing the full potential of the new methodology, which may be best suited for the reconstruction of transmission trees in more localized settings. Nonetheless, the results suggest that SeqTrack can contribute to a better understanding of the spatiotemporal dynamics of emerging pathogens, even at a worldwide scale. The results are largely in line with the general epidemiological understanding of the spatiotemporal spread of the 2009 A/H1N1 pandemic. We also recover individual Reconstructing disease outbreaks T Jombart et al ancestries that seem sensible and correlate with human flight data. It is not entirely straightforward to compare our reconstruction with previous phylogenetic work based on sequence data from the 2009 A/H1N1 influenza pandemic (Fraser et al., 2009; Parks et al., 2009; Rambaut and Holmes 2009; Smith et al., 2009; Lemey et al., 2009b) . These authors used a smaller set of isolates and did not specifically aim to reconstruct the spatiotemporal dynamics with the exception of Lemey et al (2009b) , who analyzed 242 isolates sequenced for the HA and NA genes. They also recovered a strong connection between Mexico and Texas and multiple instances of transmissions from the United States and Canada to outside the Americas. In contrast to their results, we infer a larger proportion of direct transmissions from North America to other continents. For instance, although we infer several direct transmissions from North America to China, their reconstruction points to China being only indirectly connected to the United States through either Russia, Europe or South America.