Indigo suffruticosa Mill., commonly known as Guatemalan indigo or anil indigo, is being investigated as a regenerative rotational crop that is used to produce natural plant-based dyes in the USA. The fashion and textile industry currently rely on harmful synthetic dyes to color fabric. To improve the viability of Indigo and to minimize production costs, methods to improve Indigo seed germination rates will benefit the quality, crop yields, and enable large scale field plantings.This study was initiated to develop a methodology of treating seeds to increase seed germination rates of Guatemalan Indigo and decrease fungal seed pathogens. All studies were conducted on the currently available commercial Indigo varieties. Sterilization and germination methods included: ethanol and bleach sterilization, mechanical scarification (coffee grinder, belt sander), gibberellic acid, dry heat, freezing, distilled water soaking, and boiling water. Each treatment was replicated four times for each of the various times and temperatures tested. The dry heat method at 80°C for 30 min resulted in the highest average germination rate of 83 %. Trials demonstrated that the dry heat method was the only treatment that resulted in higher germination rates than control treatment with an average of only 64 % germination. Dry heat at 90°C across all time intervals (30 min, 1 h, and 2 h) showed no results higher than 34 % germination. Pre-treating seed with 10 min soak in 10 % bleach resulted in complete control of surface pathogens with no decrease in seed germination. The boiling water method for 30 sec also lead to higher germination rates but may prove too difficult in larger volumes. Other methods of sterilization, gibberellic acid, freezing, mechanical scarification, and long-term soaking resulted in average germination percentages equal to or less than the control of no treatment. The dry heat method should be applied 2 h before planting. Applying a 10 min bleach sterilization step and dry heat treatment will greatly improve germination of Indigo and will allow for a commercially viable protocol to be created. This will allow natural indigo to compete with inexpensive synthetic dyes, enabling producers to direct seed indigo rather than costly transplant production.