Species delimitation is fundamental to deciphering the mechanisms that generate and maintain biodiversity. Alpha taxonomy historically relied on expert knowledge to describe new species using phenotypic and biogeographic evidence, which has the appearance of investigator subjectivity. In contrast, DNA‐based methods using the multispecies coalescent model (MSC) promise a more objective approach to describing biodiversity. However, recent criticisms suggest that under some conditions the MSC may over‐split lineages, identifying species that do not reflect biological reality. Here, we reconcile these approaches using empirical data for the Greenthroat Darter complex (Etheostoma lepidum), a small freshwater fish species with a disjunct distribution in Texas and New Mexico, USA. We demonstrate that MSC methods recognizes all nine sampled populations as distinct species, sometimes splitting specimens from a single locality into multiple species. However, environmental, phenotypic and biogeographic evidence do not corroborate the nine species supported by the MSC. Instead, collective evidence indicates that E. lepidum is comprised of just three species that are consistent with the molecular phylogeny: Etheostoma lepidum (Greenthroat Darter) in rivers draining the eastern Edwards Plateau, Etheostoma cf. lepidum (Texas Darter) in the Concho and San Saba rivers and Etheostoma cf. lepidum (Pecos Darter) in the Pecos River. The Pecos Darter is likely highly imperiled due to its localized distribution and reliance on vanishing spring‐fed stream habitats. The impending biodiversity crisis makes integrative and swift species delimitation more necessary than ever. Our study exemplifies how classic taxonomic expertise combined with molecular phylogenetics can produce a more robust description of threatened biodiversity.

DNA alignments

Alignments for 1 mtDNA gene cytochrome b (cytb) and 13 nuclear loci: the first intron of the S7 ribosomal protein and protein coding exons ENC1, Glyt, ptr, RAG1 exon 3, SH3PX3, Sidkey, sreb2, tbr1, UBE3A, UBE3A-like, zic1, and ZNF503. (alignments.zip)

RADSeq concatenated alignment

Concatenated alignment of 5,336 RADseq loci. Data from MacGuigan and Near (2019). (Elepidum_RADSeq.phy)

RADSeq unlinked SNPs

Concatenated alignment of 4,707 unlinked (1 per locus) RADseq SNPs. Data from MacGuigan and Near (2019). (Elepidum_RADSeq_unlinkedSNPs.phy)

Meristic Dataset

Dataset of meristic traits for Etheostoma lepidum. See text for description of traits (Elep_meristicsFINAL.csv)

Morphometric TPS File

Original TPS file (Elep.tps), unbent TPS using 5 lateral line landmarks (Elep_unbend_5LM.tps), specimen data (photoData_final.txt), and sliding landmark data for geomorph (sliders.txt).

Environmental Dataset

Environmental dataset for Etheostoma lepidum historic localities. See text for description of variables. (Elep_allLocs_finalGeoref_noDups_envData.csv)

Tree Files

Tree files produced by various phylogenetic analyses. See text for details.