Alto Tajo Natural Park is a protected area in Central Spain. Mainly well-drained limestone country, this area has traditionally held abundant white-clawed crayfish populations. Nevertheless, its occurrence has decreased during the last few decades because of different factors. To address the scarce information on the species, an extensive survey including habitat characterisation was carried out during the summer of 2008, sampling 116 water bodies. Using a combination of survey techniques, a total of 23 populations in different degrees of conservation was found. Crayfish mainly inhabited headwater stretches less than 1 km in length, together with small ponds. A significant proportion of these populations could be related to previous stocking events. The present study revealed a high degree of isolation, with populations showing a fragmented distribution pattern. The information obtained might be used to discriminate the most adequate localities for future stocking actions, hopefully improving the success of this management tool.