In the past 400 years, there has been a drastic decline in the number of endemic species on mainland Mauritius, with the island losing 69% of its original reptile community. Of 17 endemic species, only five mostly Phelsuma species survived the human mediated disturbances on mainland Mauritius. These remaining arboreal endemic geckos still play important ecological roles in the Mauritian ecosystem. However, habitat fragmentation and introduction of invasive species have increased the threats to these endemic geckos. The recent invasion of the bigger Phelsuma grandis (giant Madagascar day gecko) has increased the threats posed to the existence of endemic geckos, while habitat loss and fragmentation is also playing a major role in gecko decline, particularly for Phelsuma guimbeaui (lowland forest day gecko). In this thesis, I studied the ecological effects of P. grandis on endemic geckos at a landscape and local scale using species .distribution and binomial mixture models. I also designed markers from microsatellite and mitochondrial DNA to research the population. genetics of P. guimbeaui in response to habitat fragmentation. Finally, I explored habitat selection of P. guimbeaui to find suita~le sites for potential translocations. First, I showed that P. grandis shared many characteristics of an invasive species and could persist in a relatively large range of environmental conditions. The results highlight that P. grandis and endemic gecko distributions can overlap. Where P .. grandis has invaded areas occupied by endemic geckos, the abundance of the Mauritian species has declined by an average of 89%. This study provides strong evidence that P. grandis and endemic geckos are unlikely to coexist in sympatry. Second, I designed arid amplified 44 markers from an enriched-microsatellite genomic library. They were tested on ten subpopulations and 20 were selected to examine the population genetics of the fragmented population of P. guimbeaui. Here, the microsatellite results suggested that most subpopulations were genetically different, with low effective population sizes and no migrations, while simulations showed that the different subpopulations were at high risks of losing genetic diversity and extinction. Mitochondrial DNA showed that the fragmented subpopulations used to be part of a panmictic population. Using the findings of this genetic study, 12 subpopulations were identified as viable and 18 subpopulations were at high risk. Third, I showed that P. guimbeaui males had a larger home range than females and males overlap more with females than males and geckos selected habitats with higher plant diversity, with trees that had taller and larger trunks and a higher cavity density. Adult geckos selected different habitat features compared to sub-adults and juveniles. The findings of this research were synthesised into a review to formulate the conservation assessment of the endemic geckos on mainland Mauritius.