The NSF Assembling the Tree of Life Project for Diptera FLYTREE has completed its second year. Current progress and developing products are summarized. Among the many ongoing projects within FLYTREE, significant progress has been made in phylogenetic data capture for mitochondrial and nuclear genes, and for comparative morphology. Early results in these areas suggest that many previously hypothesized fly lineages are well-supported by multiple lines of evidence. Exciting new findings for the earliest diversification of flies are presented.