MLLPA is a new Python 3 module developed to analyse phase domains in a lipid membrane based on lipid molecular states. Reading standard simulation coordinate and trajectory files, the software first analyse the phase composition of the lipid membrane by using Machine Learning tools to label each individual molecules with respect to their state, and then decompose the simulation box using Voronoi tessellations to analyse the local environment of all the molecules of interest. MLLPA is versatile as it can read from multiple format (e.g. GROMACS, LAMMPS) and from either all-atom (e.g. CHARMM36) or coarse-grain models (e.g. Martini). It can also analyse multiple geometries of membranes (e.g. bilayers, vesicles). Finally, the software allows for training with more than two phases, allowing for multiple phase coexistence analysis.