Ballota undulata, B. kaiseri, and B. saxatilis are very rare species grow in small-sized populations. As small populations tend to be subject to an increased probability of stochastic extinction due to demographic, environmental and genetic factors, this study aimed to figure out if Ballota populations suffer reduced fitness and its correlation or association with genetic diversity and mating parameters. Also, it aimed to investigate if there is significant difference in fitness between the three species of Ballota. Correlations and association between fitness, population size, genetic variation, and mating system parameters were tested using Spearman correlation and simple regression analyses. Stepwise regression analyses were used to identify useful predictors for fitness. The results revealed that Ballota populations' fitness is generally low to very low with no significant difference between the three Ballota species. There was no detected relationship between B. undulata fitness or population size and observed or expected heterozygosity. While there was no evidence for reduced fitness in Ballota populations, the study indicated that fitness is negatively associated with single locus outcrossing rate (ts) implying that Ballota populations are locally adapted. Population size was associated only with the number of alleles (A) and number of alleles per polymorphic locus (AP).