The DNA banding pattern of 11 human and four animal isolates (two beaver, one cat, and one guinea pig) of Giardia were compared by using two related techniques. Patterns were compared after endonuclease restriction of DNA followed by agarose gel electrophoresis and ethidium bromide staining and after Southern blot analysis using recombinant plasmids containing Giardia DNA as probes. Two major groups could be distinguished with ethidium bromide staining of eight isolates. Southern blot analysis, however, could distinguish nine different patterns among the 15 isolates studied. One common banding pattern was seen in six isolates (two animal and four human); the remainder of the isolates were unique, with the exception of two identical isolates from sisters. Three isolates (one from a beaver and two from humans) were markedly different from Giardia with the common banding pattern, whereas the other six unique isolates varied moderately. Beavers and other mammals do not seem to possess their own species of Giardia. This methodology introduces a way of distinguishing one species of Giardia isolate from another and promises to be helpful in epidemiological investigations.