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The analysis of transionospheric Radio Frequency (RF) signals, such as those transmitted by Global Navigation Satellite Systems (GNSS), is a well-established technique to monitor ionospheric irregularities and ionospheric scintillations. Unfortunately, these signals are susceptible to RF interferences (RFI), and misleading ionospheric scintillation indices may be estimated due to intentional and unintentional disturbances. This paper presents the results of an intensive, on-field campaign of observation and recording of GNSS signals in the Mediterranean Area. One year of continuous monitoring allowed for the characterization of an actual RFI centered on the L1/E1 GNSS band. The results demonstrated that high-intensity occurrences of such an RFI invalidated the ionospheric scintillation indices calculated by a GISTM (GNSS Ionospheric Scintillation and TEC Monitoring) receiver installed at the atmospheric observatory in Lampedusa (Italy). According to the RFI features, the study discusses its nature by hypothesizing a Frequency-Hopping (FH) or Multiple Frequency Shift Keying (MFSK) modulated signal that may act as a complex jamming interference with randomized, short subtones. Therefore, a model of the detected interference is presented to support further works on detection and mitigation techniques as well as a deeper understanding of its effect against GNSS receivers to a large extent.