Background <p>Aerobic Anoxygenic Phototrophic (AAP) bacteria are an essential component of aquatic microbial communities and play an important role in carbon cycling due to their ability to supplement their chemoorganotrophic metabolism with light-derived energy. While most of the previous studies focused on abundance, species composition and seasonal changes of AAP bacteria, their affinity for particle-attachment has received little attention. Similarly, it remains unclear whether the entire marine AAP community is phototrophically active. In this study, we investigated the community composition of free-living and particle-attached AAP bacteria in the central Adriatic Sea’s coastal waters, using both DNA and RNA <i>puf</i>M amplicon sequencing of the AAP community in the free-living and in all fractions.</p> Results <p>AAP bacterial abundance increased from 1.27 × 10⁴ cells mL⁻¹ in winter to 8.30 × 10⁴ cells mL⁻¹ in summer. Photoheterotrophy by AAP bacteria, based on BChl<i>a</i> concentration, presented higher values in summer and spring and it was consistently higher in the particle-attached fraction than in the free-living during winter and spring. DNA and RNA <i>puf</i>M amplicon analyses revealed large differences in activity among the species forming the AAP communities. Additionally, DNA-based assessments underestimated the phototrophic activity of certain genera, demonstrating discrepancies between the gene presence and its functional expression.</p> Conclusions <p>Our data demonstrate that the expression of phototrophy genes in AAP bacteria is heterogeneous and largely varies throughout seasons and fractions. Although the particle-attached fraction contained similar amount of active AAP bacteria, it harboured substantially higher photoheterotrophy than the free-living fraction in winter and spring, with seasonal shifts and lifestyle driving changes in the phototrophy gene expression. RNA and DNA libraries revealed discrepancies between total and active AAP bacterial communities, emphasizing the importance of transcript-based approaches for accurately assessing photoheterotrophic active AAP bacteria in the marine environments. The pronounced partitioning of AAP bacterial diversity and activity between free-living and particle-attached fractions indicated the ecological specialization of certain AAP lineages, which may have noteworthy implications for the consumption of particulate organic matter and, ultimately, carbon cycling in coastal waters.</p>