Mealybug, Phenacoccus solenopsis Tinsley, is a sap-sucking hemipteran insect. It is an agricultural pest that is now widely distributed in India. In this study we report the presence of Rickettsia from P. solenopsis. We constructed a 16S rRNA gene library to study the bacterial diversity associated with this insect and we found that all the clones from the library were only of Candidatus Tremblaya phenacola. This study also highlights that the normal protocol adopted to study the bacterial diversity from environmental sample, by preparation of a 16S rRNA gene library, does not work when the bacterial population is highly skewed in favor of one bacteria (primary endosymbiont in this case). Hence, we used bacterial genus specific polymerase chain reaction primers to test the presence of any of the widely known secondary endosymbionts associated with insects. We tested for the presence of Cardinium, Rickettsia, Wolbachia, and Arsenophonus in P. solenopsis collected from 10 different locations across India. Only Rickettsia was detected from four locations while we were not able to find any other bacteria. We confirmed the presence of these bacteria by localizing Rickettsia and the primary endosmbiont, Candidatus Tremblaya sp. to the bacteriocyte of P. solenopsis using fluorescent in situ hybridization.