Pinus mugo plays a significant ecological role in the natural environment at high altitudes in the mountains including the Alps, Pyrenees, Carpathians, and Balkans. In such severe conditions, it is subjected to the harmful effects of various abiotic and biotic factors. In one of the areas of its natural occurrence in Tatra Mts. (southern Poland), for the last few years, a significant intensification of needle disease has been observed. Symptoms similar to those recorded in Tatra Mts. also occur on other Pinus species in Europe and North America, where they are caused by fungi belonging to the genus Elytroderma, Lophodermella, Lophophacidium or Ploioderma (Rhytismataceae). The current paper presents the results of research which was mainly aimed at characterization of disease symptoms observed for the first time in Poland on P. mugo needles, and identification of the main causal agent with use of the morphological and molecular technique. Based on the analyses performed at different times of the year (2015–2020), it was found that dieback symptoms initially appeared only on first-year needles, a few weeks after their development. Symptoms occur on one or both needles in the bundle. The distal parts of the needles died, while the basal parts remained green. In the following year, mainly in June and July, on the previous year’s needles attached to the shoots, mature ascomata can be seen. The fungus Lophodermella sulcigena has been identified as the cause of these symptoms. So far, the related species L. conjuncta has not been found. The morphological features of the pathogen microstructure produced on P. mugo needles are presented. Attention was drawn to certain features that may make its identification difficult, especially in terms of shapes and sizes of ascospores. The phylogenetic position of the identified causal agent in relation to closely related other species was determined. The current results confirmed that L. sulcigena shows great phylogenetic similarity to L. montivaga, which is found in North America. Nine rDNA barcode sequences of L. sulcigena obtained in this work will enrich the NCBI GenBank database. The obtained results, indicating the presence of other fungi in L. sulcigena ascomata, which may limit the spread of its ascospores, were also discussed.