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.