<p>Understanding variation in life history traits, those traits that underlie rates of survival and reproduction, is important for assessing the long-term security and extinction risk of any population. Measuring life history traits is especially important for small, isolated populations exemplified by many desert fishes. We report life history variation within and among populations of the New Mexico state protected White Sands pupfish, <i>Cyprinodon tularosa</i> using life history data of somatic growth (length, wet weight, and dry weight) and reproductive allocation (gonadosomatic index, presence of eggs with yolks) from females (<i>N</i> = 775) collected during the summers of 2000 and 2001. <i>C. tularosa</i> occupies habitats that differ in water flow, salinity, and parasite communities and shows high inter-population variation in heritable body shape. We expected these ecologically divergent habitats and morphological differences may lead to similarly high inter-population variation in life history traits; however, contrary to our expectations, habitat and genetic ancestry were not strong predictors of life history trait variation. Redundancy analysis showed most life history variation occurred among individuals within habitats (&gt; 70%). Multivariate analyses of life history traits suggested one of the most important patterns in life history trait variation was an apparent trade-off between lipid storage and reproductive allocation. Further, we found that digene parasites did not directly affect reproductive traits but may have important indirect impacts on life history trade-offs. Higher parasite density and higher reproductive investment were both associated with reduced lipid content. Overall, we conclude White Sands pupfish exhibited similar life history strategies across all four populations and sacrifice energy storage to maintain reproductive investment in the presence of parasites.</p>