Fis1 is an outer mitochondrial membrane protein that has been suggested to play a role in mitochondrial morphology and apoptosis, through its oligomerization and the recruitment of Drp1 to discrete structures on the mitochondria, leading to mitochondrial fragmentation. Fis1 also triggers autophagosome formation. However, the precise role of Fis1 in mitochondrial morphology and cell signaling have been challenged by the finding of new receptors for Drp1 and the lack of a clear mitochondrial shape phenotype in knock down models of Fis1. In order to clarify these questions, we have turned our attention to the existence of Fis1 splicing variants. Here we show that mouse Fis1 gene produces three alternative isoforms, mFis1.1, mFis1.2 and mFis1.3. Interestingly, we have found that the mRNA of these variants is differentially expressed in mouse tissues. In excitable tissues such as brain and heart, mFis1.1 and mFis1.2 variants are highly expressed. Additionally, over expression of the isoforms showed that the three isoforms where mitochondrially localized and that mFis1.3 was rapidly degraded, as indicated by it stabilization upon proteosomal inhibition. Interestingly, while mFis1.1, the mouse orthologue of hFis1, and mFis1.3 induced mitochondrial fragmentation, mFis1.2 triggered mitochondrial elongation. Ablation of Fis1 in MEF cells induces mitochondrial elongation, which correlated with an increase in mΔΨ, less ROS production and a more efficient mitochondrial respiration. Moreover, Fis1 KO cells were resistant to apopstosis, suggesting that, in basal conditions, mFis1 contribute to mitochondrial fragmentation and is required for cell death. On the other hand, during starvation, mFis1.2 mRNA was up regulated 6 folds in starving cells in a PKA-dependent manner. Inhibition of the spliceosome assembly by down regulation of the spliceosome subunit U2AF65, induced reduction of mFis1.2 mRNA and inhibited starvation-mediated mitochondrial elongation, suggesting that PKA acts through spliceosome modulation to induce mFis1.2 up regulation. Finally, we show that mFis1.2 up regulation in starving cells was responsible for mitochondrial fusion, since knock down of mFis1.2 reduced mitochondrial elongation in starving cells. Hence, in this work we present a novel and opposite function for Fis1 gene, which through the use of one of its splice variants, induces mitochondrial elongation during starvation in order to optimize respiration in conditions of nutrient deprivation.