For near-future missions planed for Mars Sample Return (MSR), an international working group organized by the Committee on Space Research (COSPAR) developed the sample safety assessment framework (SSAF). For the SSAF, analytical instruments were selected by taking the practical limitations of hosting them within a facility with the highest level of biosafety precautions (biosafety level 4) and the precious nature of returned samples into account. To prepare for MSR, analytical instruments of high sensitivity need to be tested on effective Mars analogue materials. As an analogue material, we selected a rock core of basalt, a prominent rock type on the Martian surface. Two basalt samples with aqueous alteration cached in Jezero crater by the Perseverance rover are planned to be returned to Earth. Our previously published analytical procedures using destructive but spatially sensitive instruments such as nanoscale secondary ion mass spectrometry (NanoSIMS) and transmission electron microscopy coupled to energy-dispersive spectroscopy revealed microbial colonization at clay-filled fractures. With an aim to test the capability of an analytical instrument listed in SSAF, we now extend that work to conventional Fourier transform infrared (FT-IR) microscopy with a spatial resolution of 10 μm. Although Fe-rich smectite called nontronite was identified after crushing some portion of the rock core sample into powder, the application of conventional FT-IR microscopy is limited to a sample thickness of <30 μm. In order to obtain IR-based spectra without destructive preparation, a new technique called optical-photothermal infrared (O-PTIR) spectroscopy with a spatial resolution of 0.5 μm was applied to a 100 μm thick section of the rock core. By O-PTIR spectroscopic analysis of the clay-filled fracture, we obtained in-situ spectra diagnostic to microbial cells, consistent with our previously published data obtained by NanoSIMS. In addition, nontronite identification was also possible by O-PTIR spectroscopic analysis. From these results, O-PTIR spectroscopy is suggested be superior to deep ultraviolet fluorescence microscopy/μ-Raman spectroscopy, particularly for smectite identification. A simultaneous acquisition of the spatial distribution of structural motifs associated with biomolecules and smectites is critical for distinguishing biological material in samples as well as characterizing an abiotic background.