Carbonaceous matter (CM) from ca. 3.5Ga hydrothermal black cherts of the Pilbara Craton of Western Australia and the Barberton Greenstone Belt of South Africa yielded transmission electron microscopy (TEM) images that are suggestive of microbial remains and possible remnants of microbial cell walls. These are compared to a potential modern analogue, the hyperthermophilic Methanocaldococcus jannaschii, derived from an active seafloor hydrothermal environment and cultured under similar conditions. A striking resemblance to the early Archaean forms was evident in wall structure and thermal degradation mode. Cell disintegration of the cultures occurred at 100°C marking the limits of life. Complete disintegration, deformation and shrinkage occurred at 132°C. A multidisciplinary approach to the characterisation of the CM was undertaken using organic petrology, TEM coupled with electron dispersive spectral analysis (EDS), high resolution TEM (HRTEM) to determine molecular ordering, and elemental and carbon isotope geochemistry. Reflectance measurements of the CM to determine thermal stress yielded a range of values corresponding to several populations, and pointing to different sources and processes. The δ¹³C values of Dresser Formation CM (−36.5 to −32.1‰) are negatively correlated with TOC (0.13–0.75%) and positively correlated with C/N ratio (134–569), which is interpreted to reflect the relative abundance of high R_o/oxidised/recycled CM and preferential loss of ¹²C and N during thermal maturation. TEM observations, inferred carbon isotopic heterogeneity and isotope fractionations of −27 to −32‰ are consistent with the activity of chemosynthetic microbes in a seafloor hydrothermal system where rapid silicification at relatively low temperature preserved the CM.