The identification of plastid DNA markers that provide sufficient phylogenetic resolution at the species and population levels is an important challenge for plant systematics. This is mainly due to the relatively slow rate of evolution of the plastid genome. In this study, we examine the utility of several plastid DNA regions for phylogenetic inference at low taxonomic levels in tribe Lycieae (Solanaceae). The regions employed here previously provided considerable numbers of potentially informative characters in investigations of sequence variation across the plastid genome, and one region (trnH-psbA) has been advocated for use in DNA barcoding. We sequenced nine noncoding plastid DNA regions (∼8,400 bp) for a diverse sample of Lycium species and Phrodus microphyllus (tribe Lycieae), as well as the outgroup Nolana, and included published sequences from the distant outgroup Atropa. The nine regions varied with regard to their phylogenetic utility, as measured by the numbers of variable and parsimony informative characters and informative insertions/deletions. We advocate a combination of three regions, including trnD^GUC—trnT^GGU, rpl32—trnL^UAG, and ndhF—rpl32, for phylogenetic studies at the infrageneric or tribal level in Solanaceae. Collectively, these three plastid DNA regions had >100 variable characters across 24 taxa, with 72 parsimony informative characters, and 10 phylogenetically informative indels. Future studies should explore these three noncoding markers for low level phylogenetic questions in other taxonomic groups.