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Magnetic Fluid Hyperthermia mediated by iron oxide nanoparticles is one of the most promising therapies for cancer treatment. Among the different candidates, magnetite and maghemite nanoparticles have revealed to be some of the most promising candidates due to both their performance and their biocompatibility. Nonetheless, up to date, the literature comparing the heating efficiency of magnetite and maghemite nanoparticles of similar size is scarce. To fill this gap, here we provide a comparison between commercial Synomag Nanoflowers (pure maghemite) and bacterial magnetosomes (pure magnetite) synthesized by the magnetotactic bacterium <italic>Magnetospirillum gryphiswaldense</italic> of <inline-formula> <tex-math notation="LaTeX">$\langle D \rangle \approx ~40$ </tex-math></inline-formula>&#x2013;45 nm. Both types of nanoparticles exhibit a high degree of crystallinity and an excellent degree of chemical purity and stability. The structural and magnetic properties in both nanoparticle ensembles have been studied by means of X&#x2013;Ray Diffraction, Transmission Electron Microscopy, X&#x2013;Ray Absorption Spectroscopy, and SQUID magnetometry. The heating efficiency has been analyzed in both systems using AC magnetometry at several field amplitudes (0&#x2013;88 mT) and frequencies (130, 300, and 530 kHz).