One of the most important aspects of biodiversity studies on maerl is the consideration of the serious taxonomic problems involved. The algae include a high proportion of winter-fertile crustose species, which are rarely collected with the reproductive organs essential for identification. Accurate identification of epiphytic coralline algae and boring green and red algae requires a long protocol including decalcification, staining and mounting of specimens. A further problem is posed by the occurrence of heteromorphic life histories among species common in the maerl epiflora. Problems with identification of the animals present may be exacerbated by the presence of sibling species in several genera.

The frequent use of large mesh sizes for sieving of samples is another problem. Recent studies of meiofauna have shown that there may be undescribed or very rare species present, some of which may be restricted to maerl (Davies & Hall-Spencer, 1996; O'Connor & McGrath, 1997). During the course of an extensive survey of macrobenthic communities in the greater Galway Bay area, maerl locations were sampled by different methods (O'Connor & McGrath, 1997). Sampling at South Bay, off Inisheer and at Casla Bay was carried out with a dredge and the mesh size used for washing the samples was 2 mm. The macrofauna was dominated by a number of characteristic bivalve and echinoderm species, e.g. Venus fasciata and Neopentadactyla mixta. More detailed work in Kilkieran Bay based on diver-collected samples which were relaxed with menthol crystals revealed a variety of species from a number of phyla which are either unrecorded or poorly recorded from Irish waters. Many of these organisms are <2 mm and were therefore lost in earlier surveys (O'Connor & McGrath, 1997).

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