To investigate the variability in the reproductive tactics of Acigol killifish (Aphanius transgrediens), one of the most seriously threatened freshwater teleost species, this study compared its reproductive ecology in two contrasting habitats that differ substantially in terms of stability of environmental parameters, particularly salinity regime (stable vs. unstable). Fish were sampled monthly from October 2013 to September 2014 with the aim of testing whether the reproductive life-history response of fish to stable and unstable conditions differed. The reproductive effort (gonad weight) of both sexes did not differ significantly between the two habitats, but females in the unstable habitat had significantly lower fecundity and larger eggs. The relationship between fecundity and fish size was stronger in the stable habitat, whereas the relationship was quite variable and uncertain in the unstable habitat. Fish born in the unstable habitat reached their first maturity at a smaller size than those in the stable habitat. The gonado-somatic index and the duration of hydrated eggs showed that reproduction continued from February to May in both habitats; nonetheless, a second spawning event occurred during July and August in the unstable habitat, which included the reproductive contributions of YOY individuals and older generations. This study's results suggest that A. transgrediens employs varying reproductive strategies against environmental instability in its restricted unique range. This may have further implications for the ways in which habitat-specific conservation methods are used.