We have measured nucleotide variation in the CLOCK/CYCLE heterodimer inhibition domain (CCID) of the clock X-linked gene period in seven species belonging to the Drosophila buzzatii cluster, namely D. buzzatii, Drosophila koepferae, Drosophila antonietae, Drosophila serido, Drosophila gouveai, Drosophila seriema and Drosophila borborema. We detected that the purifying selection is the main force driving the sequence evolution in period, in agreement with the important role of CCID in clock machinery. Our survey revealed that period provides valuable phylogenetic information that allowed to resolve phylogenetic relationships among D. gouveai, D. borborema and D. seriema, which composed a polytomic clade in preliminary studies. The analysis of patterns of intraspecific variation revealed two different lineages of period in D. koepferae, probably reflecting introgressive hybridization from D. buzzatii, in concordance with previous molecular data. En este trabajo hemos medido la variación nucleotídica en el dominio CCID en el gen period, localizado en el cromosoma X, asociado a los ritmos circadianos, el enjambre de siete especies que conforman denominado “cluster”Drosophila buzzatii: D. buzzatii, D. koepferae, D. antonietae, D. serido, D. gouveai, D. seriema y D. borborema. Nuestro estudio mostró que la selección purificadora es la principal fuerza que gobierna la evolución de period, en acuerdo con una región que como CCID juega un papel importante en la maquinaria de los ritmos circadianos. Hemos observado que la variación en period provee información filogenética que permitió resolver la politomía que involucra a D. gouveai, D. borborema y D. seriema. Finalmente, el análisis de la variación intraespecifíca reveló la presencia de dos linajes en D. koepferae, uno de los cuales podría ser consecuencia de hibridación introgressiva desde D. buzzatii, en acuerdo con estudios anteriores en regiones génicas localizadas en otros cromosomas. Table S1. Polymorphism statistics and minimum number of recombination events applied to period gene sequences of the species of Drosophila buzzatii cluster. Table S2. Pairwise comparison of fixed differences and shared polymorphisms among the Drosophila buzzatii cluster species, where the shared polymorphism is shown in parenthesis (above diagonal). Average intraspecific (diagonal) and interspecific (below diagonal) genetic distances values were based on the Tamura and Nei model [Tamura and Nei (1993)]. Table S3. Results of Z-test of selection based on the Nei and Gojobori method (Nei and Gojobori, 1986). Figure S1. Transition (s) and transversion (v) rates plotted against divergence among sequences of the nuclear gene period based on the Tamura and Nei model (Tamura and Nei, 1993). Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.