Rodents are animals that provoke special concern in the rural and urban areas as may cause potential damage in facilities and infrastructures as well as social alarm. The control of rodent populations is based on prevention and on what it has been called an “Integrated Pest Management” strategy. The most important species affected by this strategy are brown rat (Rattus norvegicus), black rat (Rattus rattus L.) and mouse (Mus musculus). In the present work, our original objective was to monitor changes in status or range of rodent species in the Community of Madrid (Spain). We conducted in coordination with the professional organization of Pest Control Operators “ANECPLA” a procedure designed to obtain faecal samples in locations with rodenticide treatment. Determination of pest specie was based on cytochrome b (cytb) sequences and phylogenetic analysis. We received samples from a variety of locations in which a rodenticide treatment was applied due to infestation or to citizen notice. While we recorded a number of data about the distribution of brown rat the presence of black rat was unexpectedly discovered. The detection of this species implies changes in pest control strategies to improve the results in the application of rodenticides available in the market.Key MessageRodent pest control is a key issue but little is known about Spanish populations. We aimed to know how many rat species there are in Central Spain, specifically in the Community of Madrid. We found for the first time the presence of black rat and a new wild strain of brown rat in this area. These findings have change the strategies of rodent treatment and stresses the importance of population studies for a better control.