Simple Summary Leishmaniasis is a group of parasitic diseases that affect humans and animals. Climate change and increased travel and migration have contributed to the spread of leishmaniasis in Europe, which may allow the introduction of new exotic Leishmania species or change the profile of known strains. Therefore, it is a priority to continue isolating and characterizing Leishmania strains from hosts. In this study, we analyzed and characterized two Leishmania isolates (NAV and TDL) obtained from naturally infected mammals (dogs). We identified Leishmania infantum parasites, the main agents responsible for the disease in Spain and Europe. We focused on the analysis of growth rate, treatment response, infection capacity, and gene expression, comparing these isolates with the widely studied strain L. infantum BCN 150. Considering that these isolates showed different profiles, both NAV and TDL could be useful for in vitro and in vivo assays that might shed some light on the biology of the parasite. Leishmaniasis is spreading in Europe, especially in endemic countries such as Italy and Spain, in part due to ongoing climate change and the increase in travel and migration. Although Leishmania infantum is the main agent responsible for this disease in humans and animals, other species and hybrids have been detected. This highlights the need to continue isolating and characterizing Leishmania strains from biological samples of infected hosts. In this study, we characterized the recently isolated parasites L. infantum NAV and L. infantum TDL, obtained from naturally infected mammals (dogs), and we compared them with the widely distributed and studied strain L. infantum BCN 150. Both NAV and TDL promastigotes showed a slower growth rate than BCN 150 and were significantly more sensitive to amphotericin B and miltefosine. Furthermore, the expression of the CYCA gene (involved in cell cycle and proliferation) was significantly downregulated in NAV and TDL isolates. On the other hand, CYC6 (implicated in treatment resistance) and APG9 (related to the recycling of protein under stress conditions and/or while undergoing a differentiation process and treatment resistance) levels were upregulated, compared to those measured in BCN 150. Both isolates displayed a higher infection capacity (>3 amastigotes per macrophage and >70% of infected macrophages) compared to controls (<2 amastigotes/cells and <50% of infected macrophages). Finally, a higher susceptibility to miltefosine treatment was observed in intracellular NAV and TDL amastigotes. In conclusion, TDL and NAV are novel Leishmania isolates that might be useful for in vitro and in vivo assays that will allow a better understanding of the parasite biology in Mediterranean areas.