Oyster reefs occupy subtidal and intertidal zones in Florida and are mapped using a variety of methods to inform resource management. Regardless of the method used for mapping, each has its limitations resulting in the underrepresentation of certain types of reefs, which in turn can influence trend analyses used to make management decisions. For example, oyster reefs under bridges or vegetative canopy and peripheral oysters growing on vertical structures (e.g., mangrove roots, seawalls) are not visible in maps made using aerial imagery. Additionally, reefs in the shallow subtidal zone are often too shallow to be captured using sonar but too deep to be distinguishable in aerial imagery. As a result, these reefs are often excluded from maps; however, they still provide ecosystem services, contribute to the genetic population, and can be indicators of potential site suitability for restoration. Here we present four primary factors to consider when using oyster maps to inform decision making – the mapping method, the mapper’s definition of an oyster reef, the accuracy of delineation boundaries, and recognition of unmapped reefs. These factors heavily influence the resulting map, impacting both the comparability across different mapping techniques and the conclusions drawn from trend analyses. If these four factors can be considered in co-production of mapping efforts, the existing mapping techniques can be adapted to capture more accurate oyster distribution data, which will lead to more informed resource management.