Forest fragmentation affects animal population dynamics mainly by loss of habitat and disruption of animal movement. Lizard assemblages are affected by environmental changes, but, depending on their ecological needs, some species might be more vulnerable than others. The southern Amazon suffers accelerated anthropic actions replacing natural environments by farmland (crops and pasture). This region is considerably drier than most of the northern Amazon, with stational semi-deciduous forests fragmented and isolated by pasture, and crops to a lesser extent. Here we report data on lizard assemblages using semi-deciduous forests, forest edge and the surrounding pasture in the southern Amazon in Mato Grosso, Brazil. Lizards were collected in 21 forest fragments (41 to 7,035 ha) surrounded by pasture; using pitfall traps placed on a degradation gradient - from pasture inwards forest fragment (up to 200 m). We collected 242 individuals (14 species, seven families) in 6,300 trap-days. The pattern of species occurrence was largely nested and this nesting was associated with three habitat guilds (generalist, edge-tolerant, and forest species). Although there was no obvious fragmentation effect on lizards diversity community-wise, Hoplocercus spinosus, Bachia dorbignyi, Micrablepharus maximiliani and Kentropyx calcarta were more vulnerable to such effects than all other ten species collected. We verified that assemblages inhabiting pasture and forest edge are a nested subset of assemblages from the forest core. The remnant native vegetation is not distributed homogeneously and lizards species can persist in different parts of the landscape, therefore we recommend the protection of forest remnants as an important conservation action for lizards of the southern Amazon.