Restriction endonuclease DNA fragment patterns have been used to examine the relationships among 28 isolates of Leishmania as well as Crithidia, Endotrypanum, and Trypanosoma cruzi. Fragments of nuclear DNA were generated with six restriction enzymes, and blots were hybridized with probes from three loci. Among the major lineages the fragment patterns are essentially completely different, while within the major lineages various degrees of divergence are found. Molecular evolutionary trees were constructed using the method of Nei and Li to estimate the percent nucleotide sequence divergence among strains from the fraction of fragments shared.Defined groups, such as species or subspecies within the major lineages, are also grouped by nuclear DNA comparisons. Within the donovani complex, we find Leishmania donovani chagasi and Leishmania donovani infantum to be as similar as strains within Leishmania donovani donovani, consistent with the proposal by other workers that New World visceral leishmaniasis originated quite recently.Protozoans belonging to the genus Leishmania are frequently parasites in humans, causing a spectrum of diseases whose severity ranges from mild through severely disfiguring to lethal (1). A variety of clinical, biological, and geographical criteria were initially used to classify species (1). With further study it became evident that geographical and pathological criteria were often inadequate to discriminate among different isolates, and biochemical and molecular approaches were employed, including comparisons of isoenzymes (2-5), kinetoplast DNA (6-9), proteins (10), and antigens (11)(12)(13)(14) Comparisons of nuclear DNA have been successfully employed in other organisms for the estimation of temporal and cladistic relationships of species (18)(19)(20). We used Southern blot hybridization with various defined nuclear DNA probes to obtain data that was analyzed by the method of Nei and Li (21) to estimate first the fraction of DNA fragments shared among species and then the percent of nucleotide sequence divergence. This method yields results that generally agree with comparisons of DNA sequences or of other parameters (refs. 20,22,and 23; personal communication). However, the calculation of percent divergence assumes that all fragment differences are attributable to point mutations. This assumption may not always be valid for nuclear DNA, where the presence of detectable length mutations would lower the fraction of fragments shared between two species and thus inflate the estimate of sequence divergence (24). To detect any anomalies caused by length mutations, we examined three independent regions of the nuclear genome and analyzed each data set separately as well as in combination. Our analysis indicates that the fragment comparison method is indeed suitable for comparisons within the major lineages of Leishmania.