Spermatozoal cells are known to contain a wide variety of both coding and non-coding transcripts, but the physiological role of these transcripts is not fully understood. Therefore, the overall aim of this study was to characterize both coding and non-coding transcripts contained in ovine spermatozoa, and identify differences in expression patterns between three different sheep breeds (Merino, Dohne and Poll Dorset), and ejaculates that vary in quality. A variety of coding (e.g. MVK, PAMR1, ATP2A3, KLK12, etc.) and noncoding transcripts (e.g. XLOC_025216, XLOC_048757, XLOC_001809, XLOC_025093, etc.) were found to be differentially expressed in different sheep breeds and ejaculates of contrasting quality. Some of these transcripts have been reported to be associated with spermatozoal function or physiology in the literature. Overall, these results provide novel insights into spermatozoal transcriptomes in sheep, and also potentially indicate their functional relevance.