In a nationwide Swedish survey, 967 honey bee colonies from 521 beekeepers were sampled in the spring of 2007 and the samples assayed for Nosema spp. infections. Of the 319 positive samples, only 32 samples contained a proportion of N. ceranae DNA in mixed infections with both Nosema spp. above the cut-off point chosen for comparisons of 1%. Only one pure N. ceranae infection was found, with the rest 284 infected samples assayed being pure N. apis infections. In 2009 and 2011, beekeepers or bee inspectors providing N. ceranae mixed positive bee samples in 2007 were again asked to submit samples (2009, n = 96; 2011, n = 83). No trend of an increased proportion of N. ceranae-infected samples could be found. The proportion of N. ceranae DNA in samples with mixed infection did not increase between 2007 and 2011. It is concluded that N. apis is still the dominating Microsporidia infection in honey bees in Sweden and that there is no tendency for one species replacing the other.