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High‐throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50‐ to 100‐fold more loci than those generated using traditional Sanger sequencing‐based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single‐tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon‐based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands‐on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate …