Mitochondria are dynamic organelles that undergo cycles of fission and fusion. In the fission yeast, Schizosaccharomyces pombe, mitochondria align with microtubules and mitochondrial integrity is dependent upon an intact microtubule cytoskeleton. Here we show that mitochondria re-organize during the cell cycle and that this process is both dynamin- and microtubule-dependent. Microtubule depolymerization results in mitochondrial fragmentation but only when the dynamin-related protein Dnm1 is present. Mitochondrial fusion is, on the other hand, microtubule-independent. dnm1Delta cells, besides showing extensively fused mitochondria, are specifically resistant to anti-microtubule drugs. Dnm1-YFP localizes to foci at sites of mitochondrial severing which occupy the interface between adjacent nucleoids, suggesting the existence of defined mitochondrial "territories," each of which contains a nucleoid. Such territories are lost in dnm1Delta in which nucleoids become aggregated. Mitochondrial ends exhibit motile behavior, extending towards and retracting from the cell poles, independently of the cytoskeleton. We conclude that: (a) mitochondria are organized by microtubules in fission yeast but are not moved by them; (b) Dnm1 mediates mitochondrial fission during interphasic growth and at cell division; (c) the interaction between microtubules and mitochondria, either directly or indirectly via Dnm1, not only modifies the disposition of mitochondria it also modifies the behavior of microtubules. Cell Motil. Cytoskeleton 2009. (c) 2009 Wiley-Liss, Inc.