New biomarkers that are directly associated with canine ovulation would be of value to ensure mating on optimal days of heat. In this study, canine plasma and serum were analyzed with liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) to quantify a broad range of oxylipins for the purpose of developing a method for biomarker discovery studies in canine reproduction. A majority of the 67 oxylipins probed for were detected at comparable levels in both sample types, but more oxylipins at higher concentrations were detected in serum than in plasma. Nine of the oxylipins were detected in a pilot study of serum at levels that significantly differed (p ≤ 0.1) between time-points before (n = 10), during (n = 10) and after (n = 10) ovulation, and might serve as putative biomarkers for canine ovulation. One oxylipin (20-HETE) was significantly altered after adjusting for multiple comparisons. In conclusion, the results showed that the LC-ESI-MS/MS method was suitable for quantification of canine oxylipins, revealing important similarities and differences between plasma and serum profiles as well as preliminary ovulation-specific changes in a subset of the investigated oxylipins.