Diversification during the Pleistocene is thought to have contributed significantly to taxonomic diversity at high latitudes. In some cases this diversity is cryptic, in that speciation has occurred with little change in phenotype. We examined the genetic signatures of one such case, between American and Pacific golden-plovers (Pluvialis dominica and P. fulva, respectively). This high-latitude species pair is morphologically very similar, and they are obligate long-distance migrants. They were only relatively recently recognized as separate species. We used 1,041 bp of the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) from 20 dominica and 22 fulva and 242 amplified fragment length polymorphisms (AFLPs) from 29 individuals of each species sampled from sympatric and allopatric breeding populations to assess the levels of divergence, divergence date, and gene flow. A divergence date of ∼1.8 mya was estimated, and although we detected a seemingly old hybridization event, very little gene flow was detected (effectively zero). Significant genetic divergence was found between species (4.7% uncorrected sequence divergence in mtDNA; F_ST  =  0.21 in AFLPs). We suggest that ecological factors and possibly sexual selection acted to limit gene flow during the divergence of these cryptic species during the Pleistocene, but given the age of the split we could not determine the mode of speciation that occurred.