Although carbon is negatively related to greenhouse gas emissions primarily by anthropogenic activities, it is considered essential for life and ecological processes. Autotrophic carbon fixation is the primary path, whereas organic carbon enters the biosphere, a fundamental step in the biogeochemical carbon cycle on Earth. The Calvin-Benson-Bassham cycle, mainly observed in plants, algae, and some bacteria (i.e., cyanobacteria), was previously described as the sole carbon fixation pathway. Six other natural pathways for carbon fixation have been reported, including in thermophiles. So far, six out of seven cycles have been found in thermal environments and thermophilic microorganisms. Interestingly, with the advances of omics, synthetic biology, and bioengineering, several synthetic pathways have been designed, aiming to manipulate and increase the final yields for carbon fixation and the discovery of novel natural pathways. This investigation has excellent potential for biotechnological applications (e.g., agriculture, biofuel, carbon sequestration). Therefore, in this review, we aim to decipher the carbon fixation cycles in thermophiles by opening the black box of this underexplored microbial group and prospecting their diversity, metabolic, and genetic information for further utilization in the global carbon cycle and as alternatives for different biotechnology sectors.