Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly-evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza during the course of an epidemic. Here we sequenced 153 influenza pandemic H1N1/09 genomes from UK isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic, and have used the sequences, their dates of isolation and geographical location to infer the genetic epidemiology of the UK epidemic. We demonstrate that the UK epidemic was composed of many co-circulating lineages, of which at least 13 were exclusively or predominantly UK clusters. The estimated divergence times of two of the clusters pre-date the detection of pandemic H1N1/09 in the UK, suggesting pandemic H1N1/09 was already circulating in the UK before the first clinical case. Crucially, 3 clusters contain isolates from the second wave of infections in the UK, two of which represent chains of transmission that appear to have persisted within the UK between the first and second waves. This demonstrates that whole genome analysis can track in fine detail the behaviour of individual influenza lineages during the course of a single epidemic or pandemic