Hybridization is more common in actinopterygian fishes than any other group of vertebrates. This is especially true for members of the family Cyprinidae; for example, Hubbs found 68 different combinations of inter-generic and intra-generic hybridization among cyprinids collected east of the continental divide. Hybridization between two cyprinid species, the red shiner and the blacktail shiner (Cyprinella lutrensis and C. venusta), has been described in detail in Georgia where C. lutrensis is an introduced species. However, hybridization has not been thoroughly assessed where the two species are naturally sympatric. Our specific objectives were to determine the extent of ongoing hybridization between the two species using nuclear markers and morphometrics and to determine the extent of historical introgression using mitochondrial DNA (mtDNA). We collected 100 individuals from four different locations along the Bosque River and an additional 100 individuals from four locations along the Paluxy River. We used amplified fragment length polymorphism (AFLP) to verify species identification and determine hybrid status of each individual. A total of 56 AFLP fragments were scored, with 82.14% (47 fragments) being polymorphic (95% criterion). Based on these nuclear markers, we only identified two hybrids out of the 200 specimens analyzed; one from the Bosque River, Texas and one from the Paluxy River, Texas. There were no instances of introgression of mitochondrial DNA (mtDNA) from one species into the nuclear background of the other species. We did, however, discover the sympatric occurrence of three mtDNA lineages of C. lutrensis within a single nuclear gene pool; there was only one mtDNA lineage of C. venusta. Overall body shape was assessed using a truss network and was found to be statistically different with red shiner having the shorter and deeper body. The minimal amount of hybridization inferred from AFLP data, in combination with the absence of mtDNA introgression and limited morphological overlap, indicates that pre- or postzygotic isolating mechanisms effectively minimize genetic exchange between naturally sympatric populations of C. lutrensis and C. venusta within these two river systems.