Despite the fact that massive outbreaks of the coconut scale insect pest, Reyne (Hemiptera: Diaspididae) are inflicting significant economic losses to the Philippines' coconut industry, little is known about the population and dispersal history of this invasive pest in the country. Here, we examined the genetic diversity, structure and demographic history of sampled from localities with reported outbreaks from 2014 to 2017. We analyzed the genetic structure of the outbreak populations using mitochondrial and nuclear markers. Both markers and all methods of population genetic structure analyses indicate clear differentiation among the populations separating the north from the southern regions of the Philippines. Very low or no genetic differentiation was observed within and amongst the populations per geographic region indicating two unrelated outbreak events of the pest originating from two genetically uniform populations isolated in each respective region. Historical data supports the resurgence of an established population in the south which could have been driven by sudden climatic changes or human-induced habitat imbalance. Our study provides valuable information on the genetic differentiation of the two groups that would be useful for developing and implementing biological control strategies against this pest in the Philippines.