We developed a probe set based on five Scrophulariaceae transcriptomes to conduct a target-sequencing approach for phylogenetic analysis of 66 species representing all recognized tribes fo Scrophulariaceae plus three genera unassigned to tribe, Androya, Camptoloma, and Phygelius.  Ten tribes are recognized based on the resulting phylogeny.  Diversification of crown Scrophulariaceae was inferred to have started in the southern hemisphere approximately 60 Ma.  A southern African origin is estimated for most tribes with two exceptions, Leucophylleae and Myoporeae.