This thesis studies two related topics in liner shipping. The first topic is the contract pricing problem for container carriers. The second part studies the interaction of the longer term contracts and the spot markets/exchanges for the same goods/services. Most containerized freight is transported under the provisions of medium term contracts between ocean carriers and shippers. One of the biggest challenges for an ocean carrier is to find optimal ways to structure the prices in those contracts. In particular, an ocean carrier would like to set the prices such that the best match between supply and demand can be obtained to maximize its profit. We propose three optimization models as decision tools that carriers can use to plan the contract price structures, as well as the anticipated freight flows and empty container flows for the period covered by the contracts. Based on the models, we propose algorithms and build decision tools that generate the following output: optimal prices to be charged for the movement of freight, the anticipated freight flows and empty flows, containers to be leased, rented and purchased, and the additional voyage capacities to be procured. The first two models are deterministic and represent the problem at different levels of detail. In addition, a three-stage stochastic model is proposed to handle uncertainties in demand rates, costs, bookings and transit times on feeder arcs. Recent developments in information technology and communication make spot transactions more economical and more convenient. Nevertheless, the incidental spot transactions still count for only a very small portion of freight transported both by the large carriers who are the leaders in implementing e-commerce and in the industry as a whole. The second part of the thesis studies models to provide insight into the effect of spot market participation rates on various economic quantities. This may have implications for freight transportation industries, such as the sea cargo industry, in which longer term contracts are still prevalent. We focus our study on the following situation. Option contracts are signed before the demand is observed. As is common in liner shipping, sellers (carriers) also sell goods/services on the spot. Buyers (shippers) may or may not buy in the spot market as a matter of policy. We investigate the effects of spot market participation on the contract market and on the surpluses of all market players. It is found that the contract market shrinks as more and more buyers participate in the spot market. However, the effects on the surpluses of different market players are much more complicated and depend on the following factors: market structure, demand variation along time, demand variation among buyers and capacity level.