Two Parkinson’s disease associated genes PINK1 and Parkin co-operate to promote the selective autophagy of damaged mitochondria. PINK1 is a kinase which phosphorylates both ubiquitin and Parkin on Ser65. This leads to Parkin E3 ubiquitin ligase activation and the recruitment of mitophagy adaptors to ubiquitylated mitochondria. On the other side, a mitochondrial deubiquitylase, USP30, can suppress this PINK1/Parkin cascade and selective small molecule inhibitors have been developed, which are entering clinical trials for acute kidney injury and Parkinson’s Disease. I will discuss new findings on how PINK1 accumulates on damaged mitochondria and how a molecular memory of this event is maintained for many hours. I will also show how we have used our knowledge of this biology to develop new methodology for testing phosphorylation dependent interactions. Mouse and fly mitophagy reporter models have indicated that the PINK1-Parkin pathway accounts for only a minor fraction of mitophagy under basal conditions. We have sought other ubiquitin E3 ligases which regulate basal mitophagy, using a CRISPR/Cas9 based screen with a bespoke gRNA library. We identified two major mitophagy suppressors as VHL and FBXL4. These E3s converge on the suppression of the “ubiquitin-independent” mitophagy adaptors BNIP3 and BNIP3L (NIX), via different mechanisms. VHL inhibits their transcription by degrading the transcription factor HIF1α, whilst FBXL4 exerts post-translational control on their stability. The mitochondrial membrane shares many facets with the peroxisome and we show that pexophagy can also be regulated by separate USP30- and NIX-dependent pathways. This provides a system for the co-ordinated turnover of these two organelles. Both pathways can be up-regulated by the NAE1 inhibitor, MLN4924, which may offer some therapeutic opportunities.