Drip irrigation systems using reclaimed water often present clogging events of biological origin. Microbial communities in biofilms from microirrigation systems of an experimental greenhouse in Almería, SE Spain, which used two different qualities of water (treated wastewater and reclaimed water), were analyzed by denaturing gradient gel electrophoresis and subsequent sequencing of amplified 16S rRNA gene bands. The most remarkable feature of all biofilms was that regardless of water origin, sequences belonging to Firmicutes were prevalent (53.5 % of total mean band intensity) and that almost all sequences recovered had some similarity (between 80.2 and 97 %) to thermophilic microorganisms. Mainly, sequences were closely related to potentially spore-forming organisms, suggesting that microbial communities able to grow at high temperatures were selected from the microbiota present in the incoming water. These pioneer results may contribute to improve management strategies to minimize the problems associated to biofouling in irrigation systems.