We applied population genetic theory and statistical analysis to study the mechanism of body regeneration in Planarian flatworms. Several species of Planarians have regained attention in recent years owing to their extraordinary capacity for reconstructing whole bodies from small tissue fragments - promising to be extremely informative towards the efforts in regenerative medicine. It is estimated that stem cells comprise about 30% of their body but details of the regeneration process are largely unknown. For example, it is not clear if all stem cells or only a fraction of them close to the wound site participate actively in each round of regeneration; or whether different stem cells contribute almost equally to the growing body. Due to unavailability of transgenes for these species and lack of a high quality reference genome, many routine molecular and cell biology techniques cannot be applied to this system yet. We modeled each cell as a separate individual and the body of a worm as a population of cells. We tried to estimate the effective number of stem cells based on the temporal variance of allele frequencies across 16 generations sampled every other generations. Preliminary results proved that sequence data contain sufficient information to make the desired estimates, and generated an initial estimate of effective stem cell numbers equal to ~1.58X the number of cell generations between first and last samples (lower bound in our dataset: 22.1, more reasonable estimate is in the order of several hundred). This is a much lower number than the estimated total number of stem cells in the body indicating activity of a small fraction of them at each regeneration cycle. This project yields results to improve our understanding of body regeneration through stem cells, and emphasize the utility of out-of-the-box approaches to research when common methods fail.