Secalonic acid F (SAF) has been previously identified, however, little is known about its cytotoxic activity and related cytotoxic mechanism. The aim of this study was to evaluate the cytotoxic activity of SAF isolated from a deep sea originated fungus Penicillium sp. F11 in HL60 cells and to analyze the differences in protein expression of HL60 cells treated with SAF. The CCK-8 assay and Annexin V-FLUOS/PI assay indicated that SAF displayed dose- and time-dependent inhibition of HL60 cell proliferation and induced apoptosis. Two-dimensional gel electrophoresis (2-DE) analysis of HL60 cells treated with SAF (4 µg/ml) revealed 10 differentially expressed protein spots (P<0.05), 5 upregulated and 5 downregulated. Three spots (1 downregulated and 2 upregulated) were identified as Rho GDP dissociation inhibitor 2 (RhoGDI 2) proteins by MALDI-TOF MS. Western blotting further demonstrated the decreased abundance of full-length RhoGDI 2 together with the increased abundance of caspase 3-cleaved product of RhoGDI 2. The caspase 3 inhibitor Ac-DEVD-CHO could suppress the cytotoxic effect of SAF and significantly block the cleavage of RhoGDI 2. RhoGDI 2 is a cytosolic regulator of Rho GTPase and the caspase 3-cleaved product of RhoGDI 2 can advance progression of the apoptotic process. Our data showed that SAF may modulate RhoGDI 2 levels in HL60 cells, thereby potentially disrupting cell signaling pathways important for HL60 cell function.