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Applications of graph theory are primarily, but not exclusively, concerned with labeled graphs and various specializations of these.

Structures that can be represented as graphs are ubiquitous, and many problems of practical interest can be represented by graphs. The link structure of a website could be represented by a directed graph: the vertices are the web pages available at the website and a directed edge from page A to page B exists if and only if A contains a link to B. A similar approach can be taken to problems in travel, Biology, computer chip design, and many other fields. The development of algorithms to handle graphs is therefore of major interest in computer science. There, the transformation of graphs is often formalized and represented by graph rewrite systems. They are either directly used or properties of the rewrite systems(e.g. confluence) are studied.

A graph structure can be extended by assigning a weight to each edge of the graph. Graphs with weights, or weighted graphs, are used to represent structures in which pairwise connections have some numerical values. For example if a graph represents a road network, the weights could represent the length of each road. A digraph with weighted edges in the context of graph theory is called a network.

Networks have many uses in the practical side of graph theory, network analysis (for example, to model and analyze traffic networks). Within network analysis, the definition of the term "network" varies, and may often refer to a simple graph.

Many applications of graph theory exist in the form of network analysis. These split broadly into three categories. Firstly, analysis to determine structural properties of a network, such as the distribution of vertex degrees and the diameter of the graph. A vast number of graph measures exist, and the production of useful ones for various domains remains an active area of research. Secondly, analysis to find a measurable quantity within the network, for example, for a transportation network, the level of vehicular flow within any portion of it. Thirdly, analysis of dynamical properties of networks.

Graph theory is also used to study molecules in chemistry and physics. In condensed matter physics, the three dimensional structure of complicated simulated atomic structures can be studied quantitatively by gathering statistics on graph-theoretic properties related to the topology of the atoms. For example, Franzblau's shortest-path (SP) rings. In chemistry a graph makes a natural model for a molecule, where vertices represent atoms and edges bonds. This approach is especially used in computer processing of molecular structures, ranging from chemical editors to database searching.

Graph theory is also widely used in sociology as a way, for example, to measure actors' prestige or to explore diffusion mechanisms, notably through the use of social network analysis software.

Likewise, graph theory is useful in biology and conservation efforts where a vertex can represent regions where certain species exist (or habitats) and the edges represent migration paths, or movement between the regions. This information is important when looking at breeding patterns or tracking the spread of disease, parasites or how changes to the movement can affect other species.

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