Macroautophagy (autophagy) is a vesicle trafficking process that targets cytoplasmic cargoes to the lysosome for degradation and underlies multiple human disorders. Pioneering work in Saccharomyces cerevisiae defined the core autophagy machinery, but animals possess autophagy regulators that were not identified in yeast. Autophagic flux occurs when autophagy rate increases or decreases in response to various cellular cues, such as nutrient availability. Indeed, dysregulated autophagy rates contribute to disease, making autophagy- modulation a therapeutic avenue to treat cancer, neurodegenerative disorders, and other diseases. To identify novel regulators of autophagy in animals, I investigated autophagy in the context of animal development using Drosophila. In my dissertation, I screened for phosphoinositide phosphatases that influence autophagy, and identifed CG3530/dMtmr6, a previously uncharacterized phosphatase. CG3530/dMtmr6 is homologous to the human MTMR6 subfamily of myotubularin-related 3-phosphoinositide phosphatases. I showed that dMtmr6 functions as a regulator of autophagic flux in multiple Drosophila cell types, and the MTMR6 family member MTMR8 functions similarly in autophagy of higher animal cells. Decreased dMtmr6 function resulted in autophagic vesicle accumulation, lysosome biogenesis, and impaired both fluid phase endocytosis in the fat body and phagocytosis in embryonic macrophages. Additionally, dMtmr6 is required for development and viability in Drosophila. In human cells, lysosome homeostasis requires both the MTMR8 PH domain and catalytic cysteine residue, but only the PH domain is required to maintain autophagic flux. Collectively, this work identified a role for dMtmr6 and MTMR8 in autophagic flux and lysosome homeostasis.