The balance of mitochondrial fission and fusion (MFF) determines the size and interconnectivity of the mitochondrial "network" in the cell and it's also crucial in whether or not certain cells should die in the process of programmed cell death. MFF dynamics is not only critical for apoptosis, but also important for proper cell development and physiology. Not surprisingly, mutations in the enzymes that carry out these opposing reactions are responsible for several human diseases. MFF is regulated in part by the dynamin-related protein 1 (Drp 1), which in its active from induces mitochondrial fission. We observed that Drp1 is regulated by phosphorylation/dephosphorylation of a conserved protein kinase A (PKA) effector domain (S656). To identify the physiological role of this phosphorylation site, we transiently transfected CV1 fibroblasts with Drp1 wild-type, Drp1 mutants: S656A and S656D, and determined its effect on mitochondrial morphology using computer-assisted image analysis of immunofluorescence confocal microscopy images. A mutation of serine to an alanine residue promoted mitochondrial fission while a mutation to an aspartate residue promoted fusion. Previous attempts to score mitochondrial morphology using computer-assisted analysis [Yoon et al. (2006), Proceedings of the National Academy of Sciences 103, 2653-2658] based on circularity and aspect ratio appear to be accurate only when individual mitochondria are analyzed, namely when fission has occurred, thus this is no longer valid in certain conditions where mitochondria fuse or aggregate. We propose a novel approach to score MFF using a different set of algorithms that not only take in the account mitochondrial fission, but also fusion. We also present evidence the PP2A/PKA restructures mitochondria by phosphyorylation/dephosphorylation of Drp1 at Ser656.