We examined mating behaviour in the harpacticoid copepod Tube battagliai Volkmann-Rocco, 1972, in particular the process of delivering spermatophore seminal contents to the female urosome. Labelling using 4′6′ diamidino-2-phenylindole (DAPI) coupled with two-photon confocal laser scanning microscopy successfully visualised the spermatophore and female internal reproductive system. Sections of the female urosome were imaged to examine seminal fluid stores. The female tissues were found to auto-fluoresce as red emission under green excitation, requiring no additional tissue labelling. DAPI-labelled seminal fluid stores were identified within the female reproductive system. The details observed agreed with previous descriptions of copepod reproductive anatomy and of spermatophores. Specimens cultured under pH 8.10 and a simulated ocean acidification scenario (pH 7.67) were compared for changes in reproductive anatomy and spermatophore size and site attachment. No differences were observed in spermatophore attachment or the female reproductive system but spermatophore size was reduced significantly at pH 7.67 compared with pH 8.10. This size reduction was, however, in proportion to an overall reduction in female body size at reduced pH. Confocal microscopy is shown here to be a valuable tool to investigate detailed reproductive processes in copepods.