Sustainable management of fruit flies in any given ecology requires proper understanding of the population dynamics of key species in relation to host availability and the influence of abiotic factors. Studies were conducted to determine the phonological patterns of B. invadens and C. cosyra in the northern savanna ecology of Ghana. Fruit samples from 12 main host plants were collected from multiple sites at regular intervals between October, 2011 and September, 2013. These were maintained for pupal and adult fly emergence, and the results compared with the seasons and whether parameters. The widespread variability and abundance of fruit species in the ecology ensured year-round breeding of B. invadens and C. cosyra with different seasonal population levels. Dynamics of emergence of the flies fluctuated at various levels in response to availability of the host fruits and the influence of weather factors. Regression analysis indicated that precipitation showed the strongest influence on the fly populations. Infestation of B. invadens was positively related with temperature, relative humidity (RH) and precipitation while C. cosyra infestation was negatively related with RH. These studies provide baseline information on the natural anundance and occurrence periods of the main hosts and their influence on tephritid population patterns in Ghana. This can be useful in the development of sustainable control programmes by way of developing forecasting models for IPM decision making, applying sanitary measures, male annihilation techniques and setting up bait stations at the best period before the cropping season.