Due to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryo gel and collected intact marine snow from 100 and 400 m off Cape Blanc (Mauretania). Marine snow aggregates were fixed and washed in situ to prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of fluorescence maximum (20 m), but different from those from other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that of the fluorescence maximum. The attached microbial community structure at 400 m differed both from that attached at 100 m as well as any free-living community at the tested depths. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather than de novo colonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.