Early life histories of stream fishes are thought to influence dispersal biology and have potentially important consequences for gene flow. Documenting links of life history, larval dispersal, and gene flow is difficult because larvae of closely related species often cannot be confidently identified. In this study, field-caught darter larvae were identified to species by screening individuals for single-stranded conformational polymorphisms (SSCPs) in the control region of the mitochondrial (mt) DNA. A larval transport index (T) was compared among eight coexisting species of darters and tested for associations with adult life-history patterns and gene flow. Comparative analysis indicated that larval transport tendency was negatively associated with egg size, a result consistent with previous laboratory studies. Current velocity was also related to larval transport patterns. Etheostoma zonale larvae were more abundant than expected in high-flow habitats, whereas Etheostoma caeruleum larvae were most abundant in slow-flowing habitats, suggesting that larval fish dispersal and distribution patterns can differ greatly among closely related and ecologically similar species. Larval transport index values and gene flow were not significantly related.