This study was carried out to estimate the effect of crown closure classes (degraded forest, low crown coverage, medium crown coverage, and full crown coverage) and growth characteristics (three heights, diameter at base, diameter at breast height, and crown diameter) on cone production and to estimate fertility variation and its allied parameters in 130-year-old natural populations of Taurus cedar, also called cedar of Lebanon (Cedrus libani A. Rich.). The effect of biotic (e.g., growth characteristics, crown closure) and abiotic (e.g., light penetration, temperature, humidity, and soil characteristics) factors on cone production, fertility variation, and gene diversity was evaluated in two consecutive years of Taurus cedar. The factors, viz., altitude, temperature, aspect, and rainfall, varied, while some of them could be managed by cultural operations such as management of the crown and stand density. The impact of crown closure on cone production, fertility variation, and related parameters were observed in Taurus cedar’s natural populations sampled from southern Turkey. Maximum cone productions of 29 and 40/tree were recorded with full crown closure in two consecutive years, due to significant differences among individuals within crown closure class. For instance, cone productions were between 10 and 67 in the full crown closure of the first year. The sibling coefficient, which is a measure of the fertility variation in a stand, was the highest (1.16) for the full crown closure in the first (meaning 86% fertile trees) and the second years (1.55, 65%), while it was the lowest for the medium crown closure (1.09, 92%) in both years. Gene diversity decreased from a degraded patch (0.987) to that with full crown closure (0.984). Results of variance analysis showed a significant (p ≤ 0.05) difference between crown closure classes for cone production within the second year and between years. Significant positive (p ≤ 0.05) correlations were noted between years for cone production (r = 0.22) and between cone production and crown closure in the first and second years (r = 0.29). However, growth characteristics had no effect on cone productions in individual crown closure classes, while there were significant (p ≤ 0.05) correlations between the diameter at breast height and cone production for both years (r = 0.15 and 0.17) in pooled populations.