Blooms of haptophytes can cause fish-kills and can have major impact on the global carbon balance and on climate forcing. Large DNA viruses belonging to the Phycodnaviridae are known to control or even terminate those blooms. However, the diversity and dynamics of host and viruses are still largely unknown. Here, we compare for the first time haptophytes and phycodnaviruses along a latitudinal gradient from the Sognefjorden (Norway) and Marstrandsfjorden-system (Sweden) by 454 pyrosequencing in relation to environmental factors like nutrients, light, temperature and salinity. Haptophytes were targeted by amplification of DNA of the eukaryotic 3 µm – 20 µm size fractions with the specific primer pair Hap454. PCR of the major capsid protein gene fragments were performed directly on concentrates of the virus-size fraction (<0.45 µm). The Sognefjorden is the longest and deepest fjord in Norway and is strongly influenced both by the North Sea and glacial water, while the Swedish fjord is quite shallow and strongly influenced by the Kattegat which makes it less saline. These environmental constraints are depicted in the diversity and abundances of viruses and haptophytes.