Topoisomerases are essential for orderly nucleic acid metabolism and cell survival and are proven targets for clinically useful antimicrobial and anticancer drugs. Interest in the topologically intricate mitochondrial DNA (kinetoplast or kDNA) of Trypanosoma brucei brucei and related kinetoplastid protozoan parasites has led to many reports of type II topoisomerases that participate in kDNA metabolism (we term the T. brucei brucei gene TbTOP2mt). We have now identified and characterized two new genes for type II topoisomerases in T. brucei brucei, termed TbTOP2␣ and TbTOP2. Phylogenetically, they share a common node with other nuclear topoisomerases, clearly distinct from a clade that includes the previously reported kinetoplastid genes, all of which are homologs of TbTOP2mt. Southern blot analysis reveals the new genes are single copy and positioned ϳ1.7 kb apart. Cognate mRNAs are expressed in African trypanosomes, but only a single message is detected in Leishmania or Crithidia. TbTOP2␣ encodes an ATP-dependent topoisomerase that appears as a single ϳ170-kDa band on immunoblots and localizes to the nucleus; RNA interference leads to pleomorphic nuclear (but not kDNA) abnormalities and early growth arrest. The role of TbTOP2 is unclear. Although transcribed in trypanosomes, TbTOP2 is not detected by -specific antiserum, and RNAi silencing results in no obvious phenotype. These studies indicate that African trypanosomes and related kinetoplastid human pathogens are unusual in having independent topoisomerase II genes to service their nuclear and mitochondrial genomes, and they highlight TbTOP2␣ as a promising target for the development of much-needed new therapies.Trypanosoma brucei sp. are hemoflagellates from the order Kinetoplastida that cause African trypanosomiasis (also known as sleeping sickness) in humans and a related disease in cattle (1, 2). These diseases are fatal if untreated, and current therapies are antiquated, toxic, and limited by the emergence of drug-resistant parasites (3). New therapies are clearly needed. The parasite has two major life cycle forms as follows: insect forms with asexual and sexual stages, present in the tse-tse fly vector, and mammalian host-specific asexual bloodstream forms (4, 5). Kinetoplastids are phylogenetically ancient eukaryotes that have unusual DNA in both the nucleus and mitochondrion. The total nuclear DNA content of T. brucei brucei is ϳ2.6 ϫ 10 7 bp per haploid genome. Chromosomes, which do not condense during mitosis, are divided into the following three classes: megabase chromosomes (11 pairs), intermediate chromosomes (1-5, ploidy uncertain), and minichromosomes (ϳ100, unpaired) each carrying a single variable surface glycoprotein gene (6). Sequence and analysis of the megabase chromosomes of T. brucei brucei were reported very recently (7). The mitochondrial DNA, termed kinetoplast DNA (kDNA), 2 is a topologically complex structure that consists of thousands of minicircles and tens of maxicircles interlocked in one massive disk-shaped network. Maxic...