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The paper presents data regarding two larvae insect populations – Gomphus (Stylurus) flavipes (Charpentier, 1825) and Palingenia longicauda (Olivier, 1791), inhabiting in the communities existing at the water/sediment interface along the Danube River. The dragonfly Gomphus (Stylurus) flavipes (Charpentier, 1825) is one of the most important indicator species, listed in Annex IV of the EU Habitats Directive (EU Directive 92/43/EEC) and included in the IUCN Red List of Threatened Species, 2014. This species of dragonfly has become an endangered species in most Western European countries due to water pollution and river regulation. The other important larvae species, mayfly Palingenia longicauda (Olivier, 1791), listed in Annex II of the Bern Convention, is considered critically endangered in Europe. Both require a specific habitat conditions in order to complete their life cycle. During the spring campaigns conducted during 2012-2015, the presence of the two species was reported in 26 profiles from the Lower Danube Sector, Gomphus (Stylurus) flavipes in 18 profiles, and Palingenia longicauda in 10 profiles. The most abundant occurrences were recorded in 2015, at Km 4 – Măcin Arm (59.2 ind/ m2) for Gomphus (Stylurus) flavipes, respectively, in 2012, at Km 8 – Sf. Gheorghe) (125.8 ind/m2) for Palingenia longicauda. The presence or absence of larvae in samples, as well as their abundance, are strictly dependent on ecological conditions, the type of substrate representing the decisive factor in the microdistribution of the two larvae.