Some pathogenic microorganisms when propagated in culture medium give distinctive colors of their colonies. Such pigmentation comes in a variety of hues, and often provides important diagnostic clues in laboratories for the identification of the isolates. These microbial pigments also play a role in disease pathogenesis by interfering with host immune clearance mechanisms or by exhibiting pro-inflammatory or cytotoxic properties.

Source: http://microbeonline.com/pathogenic-microbes-characteristics-pigments-production/

Some pathogenic microorganisms when propagated in culture medium give distinctive colors of their colonies. Such pigmentation comes in a variety of hues, and often provides important diagnostic clues in laboratories for the identification of the isolates. These microbial pigments also play a role in disease pathogenesis by interfering with host immune clearance mechanisms or by exhibiting pro-inflammatory or cytotoxic properties.

Source: http://microbeonline.com/pathogenic-microbes-characteristics-pigments-production/

I know one bacteria Pseudomonas syringae, which is non-pathogenic and producing pigments. For more details on the subject please read the attached file.

There exists many non-pathogenic bacteria producing pigments, for example:  Halobacterium solarum, Streptosporangium roseum, Micrococcus roseus, Micrococcus luteus and many more.........................

Isn't Micrococcus roseus an old name for Kocuria rosea? A practical difference is that there is no literature about pathogenicity of Micrococcus roseus in PubMed while newer studies refer to infections, albeit rare and opportunistic, caused by Kocuria rosea (and Micrococcus luteus).