The oyster Crassostrea hongkongensis is eaten raw and whole, so the endogenous peptides carried by its tissue reach the intestinal lumen unprocessed; functional work on food-derived peptides has concentrated on cationic sequences. This study asked whether the endogenous peptide population of this species is anionically skewed and whether a preparation of that population alters the cytoskeletal gene programme of human intestinal epithelial cells. The published plasma peptidome of this species (PXD025247) was re-analysed, an endogenous peptide fraction below 10 kDa was prepared from oyster soft tissues without adding any protease, and the preparation was applied to differentiated Caco-2 monolayers at 0.1–2.0 mg/mL for 6–24 h; nine transcripts were measured by quantitative PCR against vehicle, protease-digested and digestion-only controls. Of 333 peptides, 157 (47.1%) carried a net charge of −1 or lower at pH 7, 148 (44.4%) were near-neutral and 28 (8.4%) carried +2 or above, and anionic peptides outnumbered cationic peptides in all four detection strata (36.4–58.3% against 4.8–9.1%). Actin-family proteins were the largest precursor source (186 peptides, 55.9%; 68.3% coverage of actin). The preparation was recovered at 2.41 ± 0.23 mg/g of wet tissues and, at 2.0 mg/mL, increased transcription of the SRF targets CCN1 (2.91-fold), VIL1 (2.29-fold), MYH9 (2.17-fold) and ACTN1 (1.83-fold) (p < 0.01 for each) and of TMSB4X, CFL1 and PFN1 (1.90-, 1.75- and 1.55-fold; q < 0.05), whereas SRF and MRTFA transcripts were unchanged; proteinase K digestion abolished the response. An endogenous peptide preparation from oyster soft tissues therefore acts on the cytoskeletal gene programme of human intestinal epithelial cells, and the anionically skewed majority of this peptidome is the fraction that warrants direct functional characterisation.