Different nematodes affect canines, however, Dirofilaria immitis is the most prevalent filariae. D. immitis causes heartworm disease that can be fatal for dogs and potentially transmitted to humans. Climate change, animal migration, among other factors have changed the dynamics of vector-borne diseases, including filariasis. In the last four years, a sudden increase of dogs with microfilaremia was reported by different veterinary centers in Cali, the main city of Southwest Colombia. The objective of this study was to molecularly identify the etiologic agent of this filariasis outbreak reported in this area from 2018-2019, using a novel PCR–RFLP method. Those filariasis cases were initially detected by microscopic and serological tests. A total of 82 canine filariasis cases were molecularly analyzed, identifying 55 (67%) of them as Acantacheilonema reconditum. PCR-sequencing was performed in eight cases confirming this finding. The filariasis cases were statistically associated with male dogs who had clinical signs of anemia, with low levels of hemoglobin and hematocrit (p <0.0001), and high levels of plasma proteins (p <0.001). This emerging canine disease constitutes an important public health concern among clinicians and advises active surveillance to explore its zoonotic potential.