Females influence offspring paternity through diverse pre- and post-copulatory mechanisms. Sperm discrimination within the reproductive tract of females is observed in insects, birds, and rodents, but current evidence among large-bodied mammals is absent. Here, we tested whether two aspects of female physiology that affect sperm survival- vaginal immune response and pH- are modulated by male genetic makeup in a nonhuman primate. This dataset includes 3 files: 1. anubis_featurecounts.Rdata : Gene count matrix created from whole transcriptome sequencing of 106 vaginal swabs and 8 semen samples. We generated RNA sequencing libraries using strand-specific library preparation with the NEBNext Ultra II RNA kit with rRNA depletion and sequenced on one NovaSeq6000 S2 100 cycle v1.5 run, generating 50 bp PE reads. We processed the raw sequencing data using the RNAseq_data_processing.sh file available at www.github.com/rachpetersen/cryptic_choice_anubis. 2. DE_sample_metadata.csv : Metadata for vaginal RNA-seq samples including 10 metrics of male genetic dviersity and mating dyad complementarity. Genotyping methods are described in detail in Petersen, R. M., Bergey, C. M., Roos, C., & Higham, J. P. (2022). Relationship between genome‐wide and MHC class I and II genetic diversity and complementarity in a nonhuman primate. Ecology and Evolution, 12(10), e9346. 3. pH_data.csv : Vaginal pH measurements with modeling metadata including male genetic diversity and genetic complementarity of the mating dyad.