Using a 15-min High Performance Liquid Chromatography (HPLC) elution program, the current study compared pigment extraction efficiencies in aerobic anoxygenic phototrophic bacteria (AAPB; Dinoroseobacter shibae, Roseobacter denitrificans, Erythrobacter longus, and a strain of Rhodovulum sp. isolated from Tagus estuarine intertidal sediments - SPS1025(T)) using four extraction times (15, 30, 60, and 120 min) and three solvents (acetone, acetone/methanol, and methanol). Overall, increasing extraction time showed no significant effect on bacteriochlorophyll a (BChl a) and carotenoid extraction efficiencies in all strains. BChl a extraction efficiency was significantly higher in the mixture acetone/methanol and methanol, but methanol induced significantly higher BChl a degradation for all strains. Carotenoid extraction efficiencies were dependent on solvent and pigment polarity. Non-polar carotenoids were better extracted with acetone and polar carotenoids with methanol. We suggest the application of the used HPLC procedure for the quantification of photosynthetic pigments in AAPB due to its high sample throughput and peak resolution. We also recommend the use acetone/methanol for extraction of AAPB photosynthetic pigments with extraction periods of 15 min to achieve higher BChl a extraction yields and minimize carotenoid degradation.