During the past 5 decades, the large-sized biota inhabiting dark marine caves has attracted the attention of many marine biologists; in contrast, studies concerning the meiofaunal organisms of these peculiar biotopes remain scanty and mostly with a taxonomic aim. In this study, the nature and abundance of meiofaunal taxa living in a Mediterranean, semi-submerged sea cave was surveyed in relation to distance from the entrance and over two different seasonal periods. Particular attention was paid to the Gastrotricha taxocene. Research was carried out in a cave along the Ionian coast of Apulia (southern Italy), the “Grotta Piccola del Ciolo” which opens for approximately 120 m on the north-eastern side of a shallow fjord and has a bottom blanketed by fine to very fine sand, occasionally rich in detritus. Quantitative samples in four replicates were collected by SCUBA diving, in November 2000 and June 2001, coring the sediment with a hand-held piston corer in three light-free sites (stations 1–3) located at increasing distances from the entrance. At each site, two additional 500-ml sediment samples were collected for an in vivo study of the Gastrotricha. Faunistic analysis found a fairly high meiobenthic diversity, identifying representatives of more than 12 major groups, with total abundances ranging from 656 ind./10 cm2 (10 cm2) in November to 1,069 ind./10 cm2 in June. Station 1, the closest to the entrance invariably hosted the most abundant meiofaunal community (851 ind./10 cm2 in November and 1932 ind./10 cm2 in June), followed by station 2 or 3 depending on the season. While nematodes and harpacticoids appear as the most abundant taxa when the cave is considered as a whole, other taxa may prevail numerically in selected stations, e.g. priapulids, which are the second most abundant taxon at station 1 (30 ind./10 cm2 in November and 83 ind./10 cm2 in June). Although the density of total meiofauna and that of the single groups may not be very high, the cave is interesting by virtue of the peculiarity of the hosted fauna, e.g., species and genera new to science or new to the Mediterranean Sea. Regarding the Gastrotricha, we found 16 species, accounting for 1.3–2.6% of the total meiobenthos (density = 8.4 ind./10 cm2 in November and 27.4 ind./10 cm2 in June). Analysis of the gastrotrich community found, particularly in June, an assemblage of taxa quite different from those found in open habitats, even at the family level; differences that are probably due to the exploitation of different food resources by animals populating the two environments, i.e. algae in the open sea versus bacteria in the caves. Results indicate that for meiofauna, as happens for macrofauna, the marine caves may represent hotspots of biodiversity and endemism; the driving forces at the base of the trophic depletion hypothesis seem to be responsible for structuring the meiofauna community inside the cave.