Drosophila has been used as a model organism to study genetic basis of biological functions for over a century. It is highly amenable to genetic manipulations and a large number of genetic resources are available to ask fundamental questions in cell and developmental biology, neuroscience, behavior and physiology. CRISPR-Cas9 based genome engineering has added to the possibilities of further fine tuning the gene manipulations and address questions that were difficult to answer until now. We have been using CRISPR based genome engineering in flies for past few years and in this talk I will discuss different kinds of such manipulations that we have been able to achieve, and the advantages and disadvantages of using CRISPR in flies over the already existing methods.