Eggs were collected in the Upper Mississippi main stem (Pool 9 and Pool 11) during the summer of 2013. Using previously published morphological characteristics, eggs were positively identified as belonging to an invasive Asian carp genus. A subsample of these eggs was subsequently analyzed using molecular methods to determine species identity. Genetic identification of a total of 41 eggs was attempted using the cytochrome c oxidase 1 (COI) gene. Due to the preservation technique used (formalin) and resulting DNA degradation, sequences from only 17 individuals could be recovered. In all cases, non-carp cyprinids were identified as the most likely species identity (usually a Notropis spp.). In previously published reports, the primary morphological characteristic that distinguishes invasive carp from non-carp cyprinids is size. However, many of the eggs that were identified as non-carp cyprinids genetically were as large as 4.0 mm in diameter (at early developmental stages), large enough to overlap in size with Asian carp eggs on the low end of their size range. Other researchers studying fish eggs and early life history stages should plan on preserving a subset of collected eggs for genetic analysis to confirm morphological identifications.