A successful regeneration protocol was developed for micropropagation of Lilium akkusianum R. Gämperle, an endemic species of Türkiye, from scale explants. The study also aimed to evaluate the effects of Meta-Topolin (mT) and N6-Benzyladenine (BA) on in vitro regeneration. The Murashige and Skoog medium (MS) supplemented with different levels of α-naphthaleneacetic acid (NAA)/BA and NAA/mT were used for culture initiation in the darkness. The highest callus rates were observed on explants cultured on MS medium with 2.0 mg/L NAA + 0.5 mg/L mT (83.31%), and the highest adventitious bud number per explant was 4.98 in MS medium with 0.5 mg/L NAA + 1.5 mg/L mT. Adventitious buds were excised and cultured in 16/8 h photoperiod conditions. The highest average shoot number per explant was 4.0 in MS medium with 2.0 mg/L mT + 1.0 mg/L NAA. Shoots were rooted with the highest rate (90%) in the medium with the 1.0 mg/L IBA, and the highest survival rate (87.5%) was recorded in rooted shoots in the same medium. The ISSR marker system showed that regenerated plantlets were genetically stable. Besides traditional tissue culture techniques used in the current study, the potential for improving the effectiveness of L. akkusianum propagation protocols by incorporating machine learning methodologies was evaluated. ML techniques enhance lily micropropagation by analyzing complex biological processes, merging with traditional methods. This collaborative approach validates current protocols, allowing ongoing improvements. Embracing machine learning in endemic L. akkusianum studies contributes to sustainable plant propagation, promoting conservation and responsible genetic resource utilization in agriculture.