Accurate detection and quantification of Candidatus Liberibacter solanacearum (CLs), the putative causal agent of zebra chip disease of potato (Solanum tuberosum L.), in the potato psyllid, Bactericera cockerelli (Sulc), has become necessary to better understand the biology of the disease cycle. Studies on the transmission efficiency of potato psyllids have shown inconsistencies with field surveys. There have also been reports of laboratory colonies inexplicably losing and regaining CLs infection as detected by polymerase chain reaction (PCR). Until now, DNA primers were used to detect CLs in potato psyllid tissue using conventional polymerase chain reaction (PCR) and gel electrophoresis or by real-time quantitative PCR. In this study, CLs was detected using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) at levels identifiable by PCR, and low levels, including samples with only one cell of CLs. Potato psyllids with <300 pyrosequencing reads did not show positive using conventional PCR. These results indicate that the currently accepted PCR diagnostic technique produces false negatives due to detection limits higher than what is generally present in field collected psyllids, and also provides an explanation as to why laboratory colonies seem to lose and regain CLs infection.