Genetic experiments involving selected strains as well as single gene mutations have provided information concerning the organization of the Drosophila circadian system. The phase of the emergence rhythm of D. pseudoobscura can be altered by genetic selection without significantly affecting the phase and period of the light-sensitive pacemaker. The period of the D. melanogaster pacemaker, over the range 19 hours to 29 hours, can be encoded in the DNA sequence of a single genetic locus. The short-period and long-period mutations do not eliminate the pacemaker's temperature compensation mechanism. The short-period mutation alters the resetting behavior of the pacemaker from weak (type 1) in wild-type to strong (type 0) in the mutant. Five aperiodic mutations isolated in D. pseudoobscura belong to two complementation groups. In complements bearing one mutation from each group, the periodicity of the pacemaker is wild-type, but the phase of the emergence rhythm is 5 hours later than wild-type. Thus mutations in particular genetic loci have dramatic effects on the basic properties of circadian pacemakers and rhythms.