Female-biased sex ratios and reproductive isolation in arthropods can be caused by endosymbiotic Wolbachia bacteria that manipulate the reproductive system of their host. Wolbachia is particularly common in terrestrial host species, but its frequency in marine arthropods is less well known. Here we asked whether Wolbachia bacteria are accountable for the female-biased sex ratio and variation in reproductive isolation levels observed in the four European species of the Jaera albifrons complex (marine intertidal isopods). We analysed the sex ratio in young adults reared in the laboratory (indicative of the sex ratio at birth), compared it with the adult sex ratio in natural populations, and performed a molecular survey of Wolbachia infection based upon amplification of three gene targets using 11 different protocols tested in 817 individuals from all species of the Jaera albifrons complex. One species (J. ischiosetosa) had a female-biased sex ratio at birth but showed no sign of infection by Wolbachia bacteria. This species, together with two others (J. albifrons and J. forsmani) also displayed female-biased sex ratio in adults in nature, while the adult sex ratio in the fourth European species (J. praehirsuta) was unbiased. A new Wolbachia strain was identified in J. albifrons and J. praehirsuta, albeit at very low frequency in populations. We conclude that Wolbachia bacteria are present in at least two species of the Jaera albifrons complex, but their prevalence is too low to have any effect on sex ratio and reproductive isolation. A sex ratio distorter other than Wolbachia may be acting in some J. ischiosetosa populations, and we hypothesize that the adult female excess seen in most species results from habitat-dependent, male-biased mortality in natural conditions.