Variation in light and temperature can influence the genetic diversity and structure of marine plankton communities. While open-ocean plankton communities receive much scientific attention, little is known about how environmental variation affects plankton communities on tropical coral reefs. Here, we characterize eukaryotic plankton communities on coral reefs across the Bocas del Toro Archipelago, Panama ´. Temperature loggers were deployed, and midday light levels were measured to quantify environmental differences across reefs at four inshore and four offshore sites (Inshore

19 Variation in light and temperature can influence the genetic diversity and structure of marine 20 plankton communities. While open ocean plankton communities receive much scientific attention, 21 little is known about how environmental variation affects tropical coral reef plankton communities. 22 Here, we characterize eukaryotic plankton communities on coral reefs across the Bocas del Toro 23 Archipelago in Panamá. Temperature loggers were deployed for one year and mid-day light levels 24 were measured to quantify environmental differences across reef zones at four inner and four outer 25 reef sites: Inner: Punta Donato, Smithsonian Tropical Research Institute (STRI) Point, Cristobal, 26 Punta Laurel and Outer: Drago Mar, Bastimentos North, Bastimentos South, and Popa Island. 27Triplicate vertical plankton tows were collected mid-day and high-throughput 18S ribosomal 28DNA metabarcoding was leveraged to investigate the relationship between eukaryotic plankton 29 community structure and reef zones. Plankton communities from STRI Point were additionally 30 characterized in the morning (~08:00), mid-day (~12:00), and evening (~16:00) to quantify diel 31 variation within a single site. We found that inshore reefs experienced higher average seawater 32 temperatures, while offshore sites offered higher light levels, presumably associated with reduced 33water turbidity on reefs further from shore. However, these significant reef zone-specific 34 environmental differences did not correlate with overall plankton community differences or 35 changes in plankton genetic diversity. Instead, we found that time of day within a site and diel 36 vertical migration played structuring roles within these plankton communities, and therefore 37 conclude that the time of community sampling is an important consideration for future studies. 38Overall, plankton communities in the Bocas del Toro Archipelago appear relatively well mixed 39 across space; however, follow-up studies focusing on more intensive sampling efforts across space 40 and time coupled with techniques that can detect more subtle genetic differences between and 41 within communities will more fully capture plankton dynamics in this region. 42