Wheat is often infected by Fusarium species producing mycotoxins, which may pose health risks to humans and animals. Deoxynivalenol (DON) is the most important Fusarium toxin in Swedish wheat and has previously been shown to be produced mainly by Fusarium graminearum. However, less is known about the co-occurrence of DON and F. graminearum with other toxins and Fusarium species in Sweden. This study examined the distribution of the most important toxigenic Fusarium species and their toxins in winter wheat (2009 and 2011) and spring wheat (2010 and 2011). DNA from seven species was quantified with qPCR and the toxin levels were quantified with a multitoxin analysis method based on liquid chromatography/electrospray ionisation-tandem mass spectrometry (HPLC/ESI-MS/MS). The method enabled detection of many fungal metabolites, including DON, zearalenone (ZEA), nivalenol (NIV), T-2 toxin, HT-2 toxins, moniliformin (MON), beauvericin (BEA), and enniatins (ENNs). It was found that Fusarium poae and Fusarium avenaceum were present in almost all samples. Other common Fusarium species were F. graminearum and F. culmorum, present in more than 70% of samples. Several species occurred at lower DNA levels in 2011 than in other years, but the reverse was true for F. graminearum and Fusarium langsethiae. The most prevalent toxins were ENNs, present in 100% of samples. DON was also common, especially in spring wheat, whereas ZEA and NIV were common in 2009 and in winter wheat, but less common in 2011 and in spring wheat. Only three samples of spring wheat contained T-2 or HT-2 above LOQ. Annual mean levels of several mycotoxins were significantly lower in 2011 than in other years, but the reverse applied for DON. The strongest correlations between mycotoxin and Fusarium DNA levels were found between F. avenaceum and ENNs (r(2) = 0.67) and MON (r(2) = 0.62), and F. graminearum and DON (r(2) = 0.74). These results show that several Fusarium species and toxins co-occur in wheat. The highest toxin levels were detected in spring wheat and DON and ENNs, the latter belonging to the group of so called "emerging toxins", which were the most prevalent toxins and those occurring at the highest levels.