The identification of species in marine benthic diatom samples remains challenging due to the limited number of comprehensive studies and the absence of modern regional floras. This issue is particularly pronounced in taxonomically complex genera such as Halamphora, which species frequently form a substantial part of benthic diatom floras. We present the observations of 23 small Halamphora species from only a handful of samples. These diatoms were part of the epiphytic and/or epizoic diatom flora in the Adriatic Sea, or found in the biofilm on plexiglass substrates in the Black Sea. With a few exceptions, most of the taxa had small valve dimensions, never exceeding 20 µm in length and only 2–3.5 µm in width. Following detailed light (LM) and scanning electron microscopy (SEM), only three of the taxa could be identified based on the literature: H. bistriata was observed in the biofilm on plexiglass substrates in the Black Sea and epizoically on the carapace of a loggerhead sea turtle in the Adriatic Sea; H. tenuicostata was detected as an epiphyte on macroalgae in the Adriatic Sea; and H. yundangensis was discovered on all sampled substrates and in both seas. Thirteen taxa were proposed as new, two of them only observed as epizoics on the carapaces of loggerhead sea turtles. Seven other unknown taxa that were found in very small numbers still await their description, once more observations become available. The study demonstrates the remarkable, yet unexplored, diversity of coastal marine benthic Halamphora species in the Adriatic Sea and the Black Sea.