With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer constrained by the limited availability of a few loci. Here, we describe a sequence capture methodology, which we used to collect data for analyses of diversification within Sabal (Arecaceae), a palm genus native to the south-eastern USA, Caribbean, Bermuda and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes for all Sabal species and two outgroup species. Sequence data were generated on an Illumina MiSeq sequencer and target sequences were assembled using custom workflows. Both coalescence and supermatrix analyses of 133 nuclear genes were used to estimate species trees relationships. Plastid genomes were also analysed, yielding generally poor resolution with regard to species relationships. Species relationships described in both nuclear gene and plastome sequences largely reflect the biogeography of the group and, to a lesser extent, previous morphology-based hypotheses. Beyond the biological implications, this research validates a high-throughput methodology for generating a large number of genes for coalescence-based phylogenetic analyses in plant lineages.