Objective:  This research examines the coevolution of languages and uniparental genetic marker (mitochondrial DNA [mtDNA] and nonrecombining Y-chromosome [NRY]) variation within five Lower Central American (Rama, Chorotega, Maléku, Zapatón-Huetar, and Abrojo-Guaymí) Amerindian groups. This pattern occurred since European contact. Methods: We examined mtDNA sequence variation from the hypervariable region 1 (HVS-1) and NRY genetic variation using short tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, and DYS439) and NRY haplogroups (Q1a3a, Q1a3*, C3b, R1b1b2, E1b1, G2a2, and I) identified through single-nucleotide polymorphisms. Phylogenetic analysis included multidimensional scaling (MDS), heterozygosity versus rii, and analysis of molecular variance (AMOVA). Results: Eighteen mtDNA haplotypes were characterized in 131 participants with 94.6% of these assigned to the Amerindian mtDNA subclades, A2 and B2. The Amerindian NRY haplogroup, Q1a3a, was present in all five groups and ranged from 85% (Zapatón-Huetar) to 35% (Chorotega). Four populations (Rama, Chorotega, Zapatón-Huetar, and Abrojo-Guaymí) were also characterized by the presence of NRY haplogroup R1b1b2 indicative of western European admixture. Seventy NRY STR haplotypes were identified of which 69 (97%) were population specific. MDS plots demonstrated genetic similarities between Mesoamericans and northern Chibchan Amerindian populations, absent in mtDNA analyses, which is further supported by heterozygosity versus rii results. Conclusions: We conclude that although these linguistically related populations in geographic proximity demonstrate a high degree of paternal genetic differentiation, recent demographic events have dramatically altered the paternal genetic structure of the regions Amerindian populations. Am. J. Hum. Biol. 25:480–490, 2013. © 2013 Wiley Periodicals, Inc.