From March to October 2006, habitat characteristics of 31, 71, 31 crocodile lizard (Shinisaurus crocodilurus) samples and 50, 90, 51 comparing samples (no crocodile lizard was found in these samples) were observed in Luokeng crocodile lizard Nature Reserve, Guangdong in spring, summer, and autumn respectively, to determine the main ecological factors affecting habitat selection in this species. The main ecological factors affecting crocodile lizard habitat selection in each season were determined by comparison and stepwise discriminant analysis of fourteen ecological factors measured in crocodile lizard samples and comparing samples in each of the respective seasons. Analysis showed that in spring, percentage of sand in the stream and vegetation coverage were the two main ecological factors affecting crocodile lizard habitat selection. A stepwise discriminant model including only these two factors yielded a predicted accuracy of 97.5%, the highest when compared to alternative models involving combinations of other sampled factors. In summer, percentage of sand in the stream, vegetation coverage, width of stream and percentage of dry branch were the main ecological factors affecting crocodile lizard habitat selection and the predicted accuracy of the model is 94.4%. In autumn, percentage of sand in the stream, vegetation coverage and food availability were the main ecological factors affecting crocodile lizard habitat selection and the predicted accuracy of the model is 97.6%. Habitats selected by S. crocodilurus in each season could be predicted with 76.7% accuracy by a model including six main ecological factors (in order of importance): food availability, distance to human disturbance, percentage of dry branch, velocity of stream water, slope of stream, and width of stream. Analysis also showed that S. crocodilurus spring, summer, and autumn habitats overlap to some extent, but that overlaps between spring and autumn were very low.