Gobiarian fishes, exemplified by gobies, sleepers and cardinalfishes, have radiated across

coastal marine and aquatic habitats worldwide, yet the biological traits deemed responsible for

generating their great diversity, such as small body size, short generation times, and

ecomorphological specialization, have also hindered resolution of their phylogeny. The current

classification of Gobiaria is based on molecular phylogenetics, and while broad relationships

among major groups have largely been settled by independent investigations, the placement of

all higher taxa have not been verified with multilocus data. The root topology recovered from

different molecular datasets is contentious, with multilocus and phylogenomic studies resolving

nursery and cardinalfishes either in reciprocal or sequential sister clades to other gobiarians,

and this deep systematic controversy questions the current two-order classification. Here I used

two complementary approaches to resolve the phylogeny of Gobiaria. In my first study I mined

public databases to assemble a sparse supermatrix of 23 genes and construct a phylogenetic

tree with dense taxon sampling, comprised of approximately 30 percent of the more than 2,400 known gobiarian species. In my second study I generated new ultraconserved element

sequence data to assemble a phylogenomic matrix of 704 genes, construct a phylogenetic tree

with comprehensive sampling of higher taxa, and estimate a timescale for diversification under

the relaxed molecular clock. Overall my studies produced more evidence in support of the

current two-order classification of Gobiaria, and revealed the root uncertainty is a result of

ancient incomplete lineage sorting. I also discovered that collared wrigglers (Xenisthmus spp.)

form a monophyletic clade separate from sleepers (Eleotridae), and recommend recognizing

family Xenisthmidae in the clade-based classification of Gobiaria. I dated origination of Gobiaria

in the youngest age of the Early Cretaceous (104 Ma), found major clades of gobies, sleepers,

and cardinalfishes diverged in the early Eocene (~50 Ma), and placed goby lineage

diversification in the Oligocene and Miocene. In summary, my studies support the current

two-order classification placing nursery and cardinalfishes in Kurtiformes and the remaining

gobiarian fishes in Gobiiformes, confirm the clade-based phylogenetic classification of gobiarian

families, and advance evidence for recognizing collared wrigglers in family Xenisthmidae.