Abstract Pigments are powerful indicators for chemotaxonomy and remote sensing studies, which are the approaches used for cyanobacterial bloom monitoring. Cyanobacterial pigments include high concentrations of phycobilins and diverse carotenoids. Filamentous nitrogen-fixing species (Nostocales) are frequent in cyanobacterial blooms of warm climate lakes, and more information about pigments can be useful for improving management. We analyzed the carotenoid ratios to chlorophyll a of nine subtropical cyanobacterial strains (orders: Synechococcales, Chroococcales, Oscillatoriales and Nostocales), for some of which we also characterized the in vivo absorption spectra (aph). The main carotenoids were β,β-carotene, echinenone, hydroxy-echinenone-like, zeaxanthin and myxoxanthophyll (including aphanizophyll and unknown myxoxanthophyll-like myxol-glycoside carotenoids); however, proportions diverged greatly between orders, a trend also observed for the aph. Zeaxanthin ratios were highest in the picocyanobacterium. Nostocales species were rich in myxoxanthophyll and echinenone, with low zeaxanthin signals. We identified four pigment assemblages differentiating the strains according to their phylogenetic orders, information that needs to be considered for tracking cyanobacterial groups, particularly Nostocales.