Invasive alien species (IAS) have always been considered as major contributors to biodiversity loss. The threat posed to global biodiversity does not cease to increase nowadays and IAS are considered as the first cause of amphibian, reptiles and mammals species decline. In this context, the invasive Lissotriton vulgaris meridionalis, native from the Italian peninsula, has progressively colonized the Ticino district (in southern Switzerland) and has since been introduced in the Geneva area. This species appears to outcompete other native newt species, therefore monitoring measures are intensively required in order to minimize its spreading. In the aim of helping herpetology experts from the KARCH (Swiss center for the coordination of the protection of amphibians and reptiles in Switzerland), we developed a specific environmental DNA (eDNA) assay to assess the presence of L. vulgaris meridionalis in Geneva canton and to survey the populations of other newt species. We performed high-throughput sequencing (HTS) of eDNA from water samples collected from 52 different ponds. Moreover, we monitored five specific ponds over the year 2017 to detect the invasive newt species in eDNA samples using quantitative polymerase chain reaction (qPCR or Real-Time PCR). We performed simultaneously HTS on those samples in order to compare the potential of two methods to detect the invasive species. Our results show that L. vulgaris meridionalis is present in 27 ponds out of the 52 initially sampled and that HTS output data agree with visual observations done by the KARCH in 75% of the ponds regarding the presence of the invasive newt. Our results concerning monitoring of the five specific ponds show that eDNA metabarcoding and qPCR are equally efficient to assess L. vulgaris meridionalis presence as both technique were able to detect the newt DNA in each sample that were part of the annual monitoring. We however obtained divergent results between the two techniques for a few samples from the 52 ponds. Thus, L. vulgaris meridionalis was detected by metabarcoding in 4 samples while considered as absent both by qPCR and visual observations, supposing that HTS might sometimes be subject to false positives when species represented by only a few sequencing reads. To conclude, we demonstrate that the eDNA approach has a great potential to be used for the detection of invasive newt species as well as to survey the populations of other newt species present in Geneva area.