Many animals develop indirectly via a larval stage that is morphologically and ecologically distinct from its adult form. Hundreds of lineages across animal phylogeny have secondarily lost larval forms, instead producing offspring that directly develop into adult form without a distinct larval ecological niche 1-7 . Indirect development in the sea is typically planktotrophic: females produce large numbers of small offspring that require exogenous planktonic food to develop before metamorphosing into benthic juveniles. Direct development is typically lecithotrophic: females produce a smaller number of larger eggs, each developing into a juvenile without the need for larval feeding, provisioned by yolk. Evolutionary theory suggests that these alternative developmental strategies represent stable alternative fitness peaks, while intermediate states are disfavored 4,8-11 . Transitions from planktotrophy to lecithotrophy thus require crossing a fitness valley and represent radical and coordinated transformations of life-history, fecundity, ecology, dispersal, and development 7,12-16 . Here we dissect this transition in Streblospio benedicti, the sole genetically tractable species that harbors both states as heritable variation [17][18][19] . We identify large-effect loci that act maternally to influence larval size and independent, unlinked large-effect loci that act zygotically to affect discrete aspects of larval morphology. Because lecithotrophs and planktotrophs differ in both size and morphology, the genetic basis of larval form exhibits strong maternal-by-zygotic epistasis for fitness 20 . The fitness of zygotic alleles depends on their maternal background, creating a positive frequency-dependence that may homogenize local populations. Developmental and population genetics interact to shape larval evolution.Streblospio benedicti females fall into two classes exhibiting classic life-history tradeoffs: Planktotrophic mothers produce small (~100um) eggs that develop into obligately feeding larvae that spend weeks in the plankton. These larvae are pelagic and grow larva-specific swimming chaetae that are thought to deter predation 21 (Fig 1a). Lecithotrophic mothers produce large (~200um) eggs that develop into larvae that do not require exogenous food and quickly leave the water column as benthic juveniles. These larvae lack swimming chaetae and a second type of larva-specific morphological structure, anal cirri containing bacillary cells, which are distinctive rhabdomeric cells of unknown function 22 (Fig 1a). There are also differences during embryogenesis 23 and organogenesis 22,24 , where accelerated development of juvenile features and truncated development of larval features occurs in lecithotrophs . Despite these developmental and larval differences, adults are indistinguishable at the level of gross morphology. Unlike examples of polyphenism, environmental input does not substantially alter egg size or subsequent offspring type 25,26 . S. benedicti is common throughout North American estuaries, but local p...