Drying operation prolong the useful life of microbial biomass and allowed more effective recovery of intracellular metabolites than the extraction of wet biomass, however these techniques can cause changes of some algal components such as carotenoids. The aim of this study was to investigate the influence of differences drying techniques on the carotenoid profile of Phormidium sp. The biomass was heterotrophically produced from agroindustrial wastewater. It was harvested by centrifugation and separated into two parts, which were submit to natural convective drying and freeze-drying. The carotenoids from each dry biomass were extracted and then separated by high performance liquid chromatography coupled to photodiode array detector (HPLC-PDA) on a C30 column. The chromatograms demonstrated the presence of fourteen different carotenoids in the Phormidium extracts, and among these, eleven were common to both extracts. Although these same carotenoids have been found in the different extracts analyzed, the proportion among they was not equivalent. While all-trans--carotene was the major carotenoid found in the extract from freeze-dried biomass (40.1%), all-trans-zeinoxanthin was the major in extract from naturally dried biomass (32.2%). Under these circumstances, the overall results indicated significantly differences on qualitative profile of Phormidium sp. dried for different methods.