The present study investigated the role of Aerobic Anoxygenic Phototrophs (AAPs) in the microbial food web along the trophic gradient, together with biological and physicochemical parameters that influenced their spatial-temporal distribution. AAPs are prokaryotes with photoheterotrophic metabolism, meaning primarily heterotrophic, but by harvesting light they can supplement a part of cellular energy requirements. Their abundance varied between 0.26 x 104 cell mL-1 at the open sea and 23.45 x 104 cell mL-1 in the Krka River estuary, while their proportion in the total prokaryotes ranged between 1.13% and 23.88%, respectively. Calculated biomass of AAPs ranged between 0.07 and 6.24 μg C L-1, with the highest values during summer in the estuarine areas and the lowest during winter in the open sea. Thus, we observed a trend of decreasing abundances and biomass from more eutrophic coastal to the oligotrophic open sea area, which confirmed the hypothesis that these organisms prefer environments with higher nutrient concentrations. Our data indicate that phosphorus limitation in the environment could be an important factor for AAP growth. The main driving factors for the whole picoplankton community variance were water column transparency, chlorophyll and salinity. Heterotrophic bacteria (HB), together with AAPs, were mainly controlled by means of predation by heterotrophic nanoflagellates (HNF) during the investigated period. On a seasonal scale, more pronounced control of HB by predators was noticed during the warmer period of the year, while on a spatial scale the strongest coupling between predator and prey was noticed in the Krka River estuary and the Kaštela Bay. The intensity of the observed coupling (D) was decreasing from the coastal to the open sea areas, where it was more noticeable during warmer research periods.