Fleas (Siphonaptera) are ectoparasitic hematophagous insects responsible for causing bites and itchy skin conditions in both humans and animals. Furthermore, they can act as vectors of different pathogens of a wide variety of diseases worldwide, including bartonellosis, rickettsiosis, and bubonic plague. Accurate identification of fleas is necessary for the study of their epidemiology, prevention, and control. In addition to traditional morphological classification approaches and molecular biology techniques, geometric morphometrics is increasingly proving to be a useful complementary tool for discriminating between Siphonaptera taxa. With the objective of determining the capacity of this technique to identify and differentiate synanthropic fleas, a principal component analysis was carried out on populations of Ctenocephalides felis, Pulex irritans, and Archaeopsylla erinacei collected in distinct regions of Andalusia (Spain). The analysis carried out on 81 male and female specimens revealed factorial maps that allowed the differentiation of the populations under study, with only partial overlaps that did not prevent their correct identification. Global size differences were also detected, with a slightly larger size in P. irritans males and a bigger size in A. erinacei females. Therefore, the present study emphasizes the role of geometric morphometrics as a useful complementary technique in taxonomic studies of arthropods, especially in the case of flea specimens lacking representative morphological features.