After the discovery in the 1940s that acid mine drainage was mainly a consequence of the metabolism of chemolithoautotrophic microorganisms able to oxidize metal sulfides, mostly pyrite, much research has been performed to understand the ecology and the physiology of the microorganisms involved. At first, to prevent this environmental problem, and later to improve the efficiency of biohydrometallurgical processes. Until recently, bioenergetic considerations focused most of the attention on the sulfur oxidizing microorganisms. The demonstration that ferric iron was mainly responsible for the oxidation of pyrite has had profound implications not only on the comprehension of the phenomena but also on the microbial ecology of the correspondent systems. The Tinto River (Southwestern Spain) is an acidic environment with a high concentration of ferric iron generated by the metabolic activity of chemolithotrophic microorganisms growing in the rich complex sulfides of the Iberian Pyritic Belt (IPB). The use of conventional as well as molecular ecology tools identified the most representative members of the chemolithotrophic community of the Tinto Basin as prominent members of the iron cycle, highlighting the importance of this element in the oxidation of sulfides. Contrary to what was expected, the sulfur cycle seems to operate with rather low efficiency in the Tinto ecosystem. Interestingly enough, anaerobic geomicrobiology seems to play an important role in the system. All these observations strongly suggest that the iron cycle is extremely important for biohydrometallurgical processes in which sulfidic minerals are involved. An understanding of the properties of these versatile microorganisms and their ecology is essential to guarantee efficient and reliable biohydrometallurgical operations.