During 2016-2017, growers at San Juan de Los Planes, El Carrizal, and El Pescadero at Baja California Sur, Mexico experienced serious outbreaks of phytoplasma squash yellowing disease, causing significant economic loss, mostly from low yield and quality of squash, Cucurbita pepo L., for export. In addition, abundant beet leafhoppers, Circulifer tenellus (Baker), presumed to transmit the disease, were observed in each field. Using nested-polymerase chain reaction (PCR) amplification of the 16S rRNA gene and comparing in silico patterns, positive Western X-disease phytoplasma of the 16SrIII group was detected. Scanning electron microscopy showed phytoplasmatic particles in sieve tubes of infected plants and insects. Phytoplasma risk based on combined data of insect abundance, disease incidence, and economic threshold was analyzed to evaluate the impact of the disease over time. Only at Los Planes with 128 adult insects per trap and 75.5% incidence of disease was risk of phytoplasma high, while at El Carrizal and El Pescadero, risk was moderate. This is the first evidence of beet leafhoppers transmitting phytoplasma to squash at Baja California Sur. The information will be useful for managing disease in the region and where squash is grown worldwide.