Ask Mr. Smarty Plants

Boy, your seemingly simple question sure turned out to be a doozy to research!  I am not a soil biologist, so please bear in mind that this is not the answer of an expert, but rather that of a gardener searching for reliable information - just like you!  The short answer is no, using molasses as a soil amendment or foliar spray in your garden should not harm any beneficial organisms living in your garden.  Molasses (both liquid and granular) is a widely accepted organic soil amendment that is used to promote biological activity in the soil by providing a readily available source of food (carbohydrates) to microbes already living in the soil.  One of your local organic gardening experts, Howard Garrett, also recommends spraying a molasses mixture onto garden plants before releasing beneficial insects (lady bugs, green lacewings and trichogramma wasps) to encourage them to stay in your garden and claims that molasses used in the garden repels fire ants.  Maryanne Caruthers-Akin, another organic gardening expert out of Portland, OR, uses molasses in her garden beds to attract earthworms - so no harm there.  The Hawaii Agriculture Resource Center says that molasses soil amendments affect the "soil microbial ecology, usually resulting in lowered populations of plant parasitic nematodes as well as having other favorable effects on plant growth.  The specific mechanisms are not well understood and vary with the crop, soil conditions, and nematode species present."  (Links are listed below.)  I have been completely unable to find any information claiming that the use of molasses will harm beneficial nematodes and it is uncertain just how molasses works to discourage "bad" nematodes.  Perhaps healthier plants are simply a less appealing target.  Whether molasses will improve your soil or not depends on how healthy and biologically active it already is, but, as long as you use it according to the instructions provided on the product, it certainly won't harm the other organisms that call your garden home.  As a side note I'd like to mention that, barring past use of chemicals that may have decreased the natural amount of biological activity in your soil, plants that are native to your area usually do not require any soil amendments to grow and thrive and are actually adapted to living in soils that are less biologically active.

Dear Dirt Doctor by Howard Garrett

Earthworms - Surprising Partners in the Creation of Healthy Soils - Tilth

Molasses Soil Amendment for Crop Improvement and Nematode Management - S. Schenk