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Premise of the study:  We developed primers targeting nuclear loci in  Castilleja  with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility.    Methods and Results:  We assembled low‐coverage genomes for three taxa in  Castilleja  and developed primer combinations for the single‐copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family. These primer combinations were designed to take advantage of the Fluidigm microfluidic PCR platform and are well suited for high‐throughput sequencing applications. Eighty‐seven primers were designed for  Castilleja , and 27 were found to have broader utility in Orobanchaceae.    Conclusions:  These results demonstrate the utility of these primers, not only across  Castilleja , but for other lineages within Orobanchaceae as well. This expanded molecular toolkit will be an asset to future phylogenetic studies in  Castilleja  and throughout Orobanchaceae.

Primers for Castilleja and their utility across Orobanchaceae: II. Single‐copy nuclear loci 1