This dataset includes information from ichthyoplankton sampling for silver carp and bighead carp collected from three main reaches in the Upper Mississippi River Basin, including the La Grange, Peoria, Starved Rock, and Marseilles reaches of the Illinois River, Pool 20 of Mississippi River, and the St. Croix River. Data include the number of bigheaded carp eggs and larvae identified using traditional manual sorting techniques, and genetic data derived from quantitative PCR (qPCR) and 4 bigheaded carp markers (SCTM4/5 and BHTM1/2) that were used to identify the amount of DNA in ichthyoplankton tow samples. These data provide information for natural resource agencies and managers who could use this qPCR screening tool to enhance traditional ichthyoplankton monitoring techniques and use the technique to quickly prioritize samples that have the highest likelihood of containing bigheaded carp eggs or larvae. Two worksheets are included in this file, including a meta-data sheet that describes the dataset, provides variable names, and associated units of measure.