Combine the yellow and brown mustard seeds. In a bowl pour the cider vinegar over the seeds and stir. Cover and store in the refrigerator or 24 hours. If seeds absorb all the vinegar too quickly add more vinegar or water as needed.
Blend the soaked seeds, garlic, honey, salt, and thyme in a blender until it is your desired consistency depending on how grainy you like your mustard.
Sterilize the jars, lids, and rings in boiling water for at least 5 minutes. Pack the mustard into the hot jars filling the jars to within 1/4 inch of the top.
Run a knife or a thin spatula around the inside of the jars after they have been filled to remove any air bubbles.
Wipe the rim of the jars with a moist paper towel to remove any food residue. Top with lids and screw on rings, refrigerate for at least 2 weeks before using.