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. ; Data files for Heyduk et al 2015 "Estimating species relationships within Sabal (Arecaceae) through multilocus analyses of sequence capture data."README for data related to Heyduk et al 2015 "Estimating species relationships within Sabal (Arecaceae) through multilocus analyses of sequence capture data." A note about gene alignment/tree naming: File names refer to the geneID from which baits were designed from. For example, "Elaeis_1007" indicates that this gene matches the exons "Elaeis_1007_*" which we submitted to MySelect for bait design. Some genes are named "Sabal" or "Nypa" because sequences from those species were submitted for the initial bait design. Files in this repository: 1) alignments.zip - folder containing alignments for all 133 nuclear genes used in ...