Many modified or degraded blanket bogs in the UK have been undergoing restoration by different rewetting strategies. While testate amoebae (TA), well-known as hydrology-sensitive species, have been increasingly applied to assess and monitor peatland restoration success, we still do not know the most appropriate sampling strategy of TA in heather-dominated peatlands. In this study, TA communities were taken from two modified blanket bog sites and one intact border mire across a strong hydrological gradient to explore the optimal sampling strategy. The results showed that: 1) TA communities from Sphagnum moss performed better to indicate the hydrological gradient of peatland habitats than other plant types (i.e., other mosses, heather and sedge litter), among which the dominant and second abundant Sphagnum moss species had similar performance as combined all Sphagnum moss did; 2) there was a clear and marked vertical separation in TA community composition, living status and species-specific niche preference; and 3) TA species richness and density incrementally increased from March to next January although median species richness decreased from September to the following January; by contrast, the average number of encysted TA was much higher in June and January than in March and September, which highlights the capability of TA to form cysts in response to extreme hot/dry and cold weather and this change may also suggest a non-negligible influence on ecosystem processes (e.g., C-cycling). Considering sampling cost and practicality, this study in heather-dominated peatlands recommends sampling the entire segment/length of the dominant Sphagnum moss from relatively flat (lawn) positions (although more studies are needed for microtopographic investigation) during the autumn or early winter as a simple but effective sampling strategy to assess the potential of TA as hydrological bioindicators or when using them to monitor the restoration (rewetting) success.