Introduced mammalian herbivores are known to be detrimental to native biodiversity and can alter ecosystem processes, by direct and indirect effects. Island systems are particularly susceptible to the impacts of such herbivores given the predator free environment for the exotic and naivete of natives. Introduced spotted deer (Axis axis), in Andaman Islands, is a potential threat to native forest floor and semi arboreal herpetofauna. In this study, we evaluated the nature and extent of this potential indirect effect on lizards from 2012 to 2014. We sampled for reptile density, arthropod abundance and understory vegetation cover across 12 islands in the archipelago with varying relative abundance of spotted deer. Spotted deer depressed the density of forest floor and semi arboreal reptiles (like the Bay Island Forest Lizard, Coryphophylax subcristatus) by reducing vegetation cover in the understory. This reduction in the vegetation cover could make the Bay Island Forest Lizard and others more vulnerable to predation and/or unfavorably alter the micro environment. The findings revealed an indirect effect of spotted deer on reptile density mediated by structural changes in the understory vegetation. This study provides evidence and impetus for the conservation of endemic and little studied reptiles in small tropical islands of Andamans by the management of spotted deer.  *Note 1* - As part of the study, eight experimental plots (exclosures to keep out deer) were set up in the evergreen forests of 4 islands to look at the effect of deer removal on vegetation and lizards. This component of the study is still in progress as long term data is required to comprehend the processes underlying observed patterns. *Note 2* - Native amphibians (e.g. Charles Darwin's frog, Ingerena charlesdarwini - Critically endangered) could also be affected by the change in the understory. This impact of the deer could not be assessed as the sampling could only be carried out in the dry season, leading to extremely low detection of frogs.