Erwinia tracheiphila (Et) causes bacterial wilt of cucurbits in the Cucumis and Cucurbita genera. Et strains fall into groups that induce rapid wilt on muskmelon versus squash; here we call these groups Et subsp. melon and Et subsp. squash, respectively. We characterized the in planta expression of Et effectors following recovery of Et subsp. melon from a primary host and a non-host, and of Et subsp. squash from primary and secondary hosts. Using qRT-PCR, we profiled the expression of 14 shared and two strain-specific effectors. An Et subsp. melon strain expressed several shared effector genes in both muskmelon and a non-host, squash. We found, however, that hrpA, which encodes the pilin protein of the type III secretion system (T3SS), was highly expressed in muskmelon but not in squash; this lack of expression of a T3SS may explain its lack of pathogenicity on squash. In fact, the Et subsp. melon effector gene expression in squash was higher than in melon, potentially due to feedback from a nonfunctional T3SS. In contrast, an Et subsp. squash strain expressed hrpA in both squash and melon, consistent with its induction of rapid wilt on squash and slow wilt on muskmelon. It also exhibited a very high level of expression of the effector gene hopO1, which is present in Et subsp. squash but not Et subsp. melon strains. Interestingly, it exhibited a 21-fold higher level of hopO1 expression in squash than in melon, consistent with HopO1 contributing to faster wilt in squash than melon.