Madagascar is a biodiversity hotspot threatened by habitat loss, which is detrimental to the future survival of forest-dwelling herpetofauna. For conservation purposes, it is essential to determine how species respond to different types of anthropogenic habitat alteration. We conducted standardized field surveys (a variation of visual encounter survey) to assess species richness, abundance and diversity among forest, clear-cut and orchard habitat types in Montagne des Français, north Madagascar. Forest sites proved to be very different from clear-cut and orchard sites with regards to habitat structure. Lizard species richness, abundance and diversity were significantly lower in clear-cut sites, with only 11% of the observed forest diversity recorded. This shift in species occurrence suggests that lizards are particularly sensitive to this type of habitat alteration. Orchard cultivation did not affect lizard species richness to the same extent, as 56% of the observed forest diversity was recorded in this habitat type. Furthermore lizard abundance was significantly higher in orchard habitat. These observations indicate that although anthropogenic activity can have an adverse effect on the lizard fauna of a given site, it will seldom lead to a total loss of diversity as species typical of pristine forest (specialists) are replaced by species adapted to secondary habitats (often generalists). Our results support the contention that anthropogenic habitat alteration can have a strong negative influence on lizard communities. Researchers should continue to identify which species may be lost or become more vulnerable in future (as a result of population decline) in response to anthropogenic habitat alteration.