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In an effort to improve our knowledge of the phylogenetic relationships among species and genera of the subfamily Sarcophaginae, we analysed data from three mitochondrial gene fragments. Sequence data for portions of the genes cytochrome oxidase I (COI), cytochrome oxidase II (COII) and dehydrogenase subunit 4 (ND4) were obtained from 43 species of Sarcophagidae representing 15 genera. We used a Bayesian approach to simultaneously choose how best to partition the data and which substitution model to apply to each partition. Phylogenetic relationships were inferred using Bayesian Inference and Maximum Likelihood methods. Our results are consistent with monophyly of the subfamily Sarcophaginae (posterior probability 1; bootstrap support 93%), as well as with monophyly of several genera within the Sarcophaginae (including Sarcophaga s.l.; posterior probability 1; bootstrap support 97%). We found support for a sister‐group relationship between Ravinia Robineau‐Desvoidy and Oxysarcodexia Townsend, which has been hypothesised by past authors on the basis of morphological similarities, although this was supported only in the Bayesian analyses (posterior probability 0. 81–0. 98), and for some novel supra‐generic clades. Contrary to a recent morphological hypothesis, we do not find Helicobia Coquillett to be nested within Sarcophaga Meigen; our data suggest, but do not strongly support, a hypothesis that Peckia Robineau‐Desvoidy is the sister group to Sarcophaga.

Correct species identification is critical when dipteran larvae are used for inference of the postmortem interval. To facilitate DNA-based identification of forensically important flies of the genus Lucilia in the continental United States, we develop a vouchered reference collection and DNA sequence database. A total of 122 specimens were collected for nine of the 10 species of Lucilia reported to occur in the continental United States. Using the polymerase chain reaction and DNA sequencing, data were obtained for an 1100-bp region of the mitochondrial gene encoding cytochrome oxidase I (COI). We consider a species suitable for DNA-based identification if it is exclusively monophyletic in >95% of bootstrap pseudoreplicate phylogenetic analyses. Seven of the nine species meet that criterion. Two species (Lucilia coeruleiviridis and Lucilia mexicana) share COI sequence and cannot be distinguished using our reference database. We conclude that DNA-based identification is likely to be successful for the other seven species.

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