This is the first study to examine the abundance of naked amoebae in the water column of a mangrove stand. A total of 37 different morphotypes was noted and at least 13 of these are probably new species. Over a one-year sampling interval, amoebae averaged 35,400 cells liter⁻¹ (range 2,000–104,000) by an indirect enrichment cultivation method. Densities in the upper end of this range are the highest ever reported for any planktonic habitat. Variation between samples was related to the quantity of suspended aggregates (flocs) in the water column emphasizing that amoebae are usually floc-associated. The study also showed that it is essential to disrupt floc material prior to withdrawing sample aliquots for the indirect counting method since several amoebae can occupy the interstices of aggregates. There is concern that indirect enumeration methods that require organisms to be cultured in the laboratory seriously underestimate the true count. A direct counting method using acridine orange staining and epifluorescence microscopy was attempted to assess the possible magnitude of the error associated with indirect counting. While this direct method had limitations, notably the difficulty of unambiguously differentiating between small amoebae and nanoflagellates, the results suggested that the indirect method gave estimates that were close to the true count (within a factor of two). Mangrove waters are rich in heterotrophic protozoa (∼ 3 × 10⁶ liter⁻¹) and while the heterotrophic flagellates are by far the dominant group, naked amoebae outnumber ciliates some 20-fold. The ecological consequences of high numbers of amoebae, particularly the common small forms less than 10 μm in length, need to be examined for these important coastal sites.