Breast cancer remains the most prevalent cancer in females. The triple negative subtype of breast cancer is associated with higher recurrence rates and poorer prognosis, lack of effective targeted therapy options, and frequently becoming unresponsive to chemotherapy. This study investigates the in vitro anti-cancer potential of our previously in silico-discovered cryptides, from Penaeus vannamei, against MCF-7, MCF-7-CR, and MDA-MB-231 cancer cell lines. Five cryptides-AD4, AD7, AD8, AD11, and AD12-were tested using the MTT assay, revealing selective toxicity against cancer cells. The lowest and highest calculated IC50 values were for AD12 against MCF-7-CR (∼4.6 μM) and MDA-MB-231 (∼20 μM), respectively. Mechanistic studies showed that the cytotoxicity mediated by cryptides, AD7 and AD8, induced loss of mitochondrial membrane potential, release of mitochondrial cytochrome C, and cleavage of caspases that were associated with BAX activation in MCF-7 and MDA-MB-231 cells. Furthermore, our results showed that both MCF-7 and MDA-MB-231 cells treated with AD7 or AD8 exhibited nuclei condensation, activation of Caspase 3/7, leading to apoptotic cell death associated with intrinsic apoptotic cell signaling mechanism. However, further investigation showed that both AD7 and AD8 peptides promoted up-regulation of FAS and p53 in MCF-7 cells while down-regulated the expression of both FAS and p53 in MDA-MB-231 cells, suggesting cell-type dependent apoptotic cell signaling mechanisms. Moreover, both AD7 and AD8 demonstrated cytotoxic and disintegration effects in 3D cancer model. This study highlights the anticancer potential of marine-derived cryptides against challenging breast cancer subtypes, including triple-negative breast cancer (TNBC), with selective cytotoxicity and potential to overcome resistance and recurrence.