Data consist of flow cytometry files (.FCS) that were generated in the analysis of larval pallid sturgeon specimens. Nuclei from produced larval sturgeon somatic cells were analyzed using flow cytometry to estimate genome size and assign ploidy. Freshly collected rainbow trout (Oncorhynchus mykiss), largemouth bass (Micropterus salmoides), or pallid sturgeon blood were used as external controls, whereby the fish blood samples were analyzed in separate tubes from the cells of prepared sturgeon larvae. All samples at 1 x 10^6 cells/mL were incubated in a propidium iodide solution to stain DNA, then analyzed by flow cytometry. Analysis software generated histograms from the experimental samples and the control standard samples. The histogram peak channels (modes) were then compared to generate a genome size estimate and additionally to visualize peaks for ploidy categorization.