The domestic dog lacks placental steroidogenesis. Thus, corpora lutea (CL) are the only source of progesterone (P4), both in pregnant and non-pregnant cycles. Due to the absence of an endogenous luteolysin in absence of pregnancy, the luteal life span in non-pregnant dogs often outlasts the length of gestation. The underlying biological mechanisms and the involvement of P4 signaling is still not fully understood. Therefore, next-generation sequencing (RNA-Seq) was performed on CL from late luteal phase and compared with normally luteolyzing CL at the prepartum P4 decrease. Briefly, functional terms related to late luteal regression were predominantly associated to extracellular matrix, transcriptional activity and steroid hormone signaling. In contrast, at prepartum luteolysis terms were mostly associated to immune inflammatory responses, including acute-phase reaction. Immune system-related events were also more highly represented in CL derived from normal luteolysis, compared with those from dogs in which luteolysis was induced. The antigestagen-effects seem to be more related to the withdrawal of P4 support than to the PGF2alpha-related inflammatory reaction observed at natural parturition. We report differentially expressed genes associated with maintenance and cessation of luteal function in pregnant and non-pregnant dogs. Based thereupon, we generated functional pathways and gene networks potentially involved in the underlying endocrine and molecular mechanisms.