The subtribe Pleurothallidinae hosts the charismatic miniature orchid genus Lepanthes, one of the largest genera in the subtribe with more than 1000 species. The majority of the Lepanthes species are found in the Andean region of Colombia and Ecuador with more than 300 species in each country. Many endemics to the northern Andes. Olaf Swartz described the genus in 1799. Species share ramicauls (stems) enclosed by a series of tubular sheaths known as lepanthiform sheaths and each bears a single leaf. Also typical of the genus are racemose inflorescences, flowers with petals usually transversely lobed, and a trilobed lip with a modified mid-lobed named as the appendix.  The footless column is adnate to the base of the lip and the stamen has two hard pollinia. Beginning in 1996 with species from Ecuador, the botanist Carlyle Luer suggested a taxonomic classification below the genus level using the morphological variation observed in sepals, including morphological features such as petals fused or free, and number of veins observed in each sepal, usually two or three. This taxonomical hypothesis has not been examined to date using phylogenetics to understand main evolutionary lines among Lepanthes species. Here we examined the maternal plastome evolution of ten Lepanthes species representing major taxonomic groups in Luer’s taxonomic classification.Plastomes had a mean length of 156,000 bp, with L. narcissus being the species with the smallest plastome size at 155,484 bp and L. caprimulgus the largest at 156,546 bp and the GC content of all plastomes was approximately 37%. All plastomes shared the same number of genes (140) and gene content (78 coding genes). We also recovered the first resolved backbone phylogeny for the genus, taking as an initial hypothesis taxonomic groups proposed by C. Luer. All analyses support the monophyly of Lepanthes (BS = 100, PP= 1), while both subgenera are paraphyletic (Lepanthes and Marsipanthes) and sections, subsections, and series are also paraphyletic.  Two main sister clades were identified. Clade 1 included two species L. narcissus(subgen. Lepanthes, subsect. Bilabiate) containing species exclusively found in Ecuador and L. caprimulgus(subgen. Marsiphantes sect. Caprimulginae) found in Ecuador and central Peru. Clade 2 includes the rest of the species representing the genus backbone. The species L. monoptera represents section Breves, which includes six species with distribution in Colombia and Ecuador, and is sister to a clade we have named core Lepanthes that includes L. manabina (series Lepanthes), L. hexapus + L. mucronata (series Mucronata) and L. eros (subsect. Breves) sister to L. felis (sect. Felinae) + L. ribes (sect. Marsipanthes). This phylogeny will accelerate evolutionary studies in this hyperdiverse genus including a large study we are developing for around 200 species. from Colombia.