From January 2001 - July 2002 the bat colony of Windsor Great Cave was monitored monthly to collect baseline natural history information, including determining the timing of breeding seasons, monitoring changes in population stage structure, and monitoring seasonal and annual fluctuations in the numbers and relative proportions of individual species. Monitoring was focused on the lower opening of the cave, through which the visitor trail passes and winds its way through the smaller of two roosting chambers, Royal Flat. The larger roosting chamber, Parnellii Roost, is not easily accessible and, consequently, human visitation and disturbance is lesser. The research was designed to identify periods when the bat colony might be most vulnerable to disturbance, enabling managers to distinguish effects of human visitation from natural population variability and, consequently, to identify best management practices for the cave. Seven hundred bats were examined during this period of research.

Windsor Great Cave hosts a minimum of 11 species of bats (Order Chiroptera), the greatest diversity recorded for any cave on Jamaica. A 12th species, the endemic Jamaican Fig-eating Bat (Ariteus flavecens) has been netted in the vicinity of the upper opening of the cave and may use the cave as a temporary roost. While generally considered to be a tree-roosting species, this bat may opportunistically roost in caves that are found in areas of seasonally-available food resources.

Eight of the 11 resident bat species were observed using the lower opening of Windsor Great Cave. The most common species were: Leaf-chinned Bat (Mormoops blainvillii, n=236), Parnell's Moustached Bat (Pteronotus parnellii; n=192); Long-tongued Bat (Glossophaga soricina; n=145), and Jamaican Fruit Bat (Artibeus jamaicensis; n=86). All of these species showed considerable monthly variation in the numbers of individuals emerging and the relative proportion of each species. Peak breeding occurred in May and June, when late-stage pregnant and lactating females were most abundant. Population numbers peaked from August through October as young bats were weaned and began foraging on their own (see diagram). The lowest numbers of bats occurred during February and March, the late-winter, dry season when food resources are thought to be most limiting, as evidenced by the poor physical condition of individuals (e.g., poorly-developed pectoral muscles, abdominal distension associated with foraging was at its lowest values).

In addition to seasonal fluctuations, the bat colony of Windsor Great Cave displayed annual fluctuations. In late 2000 / early 2001, the size of the colony decreased by 30 - 50%, as determined from visual surveys of the emergence at the upper cave opening. Ceiling occupancy in the Royal Flat roost decreased by at least 50%. However, by June 2002, the number of bats emerging from the upper opening appeared equivalent to the high number of bats observed from July - October, 2000. Additionally, there is now a small population of bats roosting in "Big Yard," a phenomenon which has not been recorded during the past seven years.

In addition to its large and diverse bat colony, Windsor Great Cave supports a rich assemblage of invertebrate species. During a supplemental survey in June 2002, 34 invertebrate species (3 Classes, 14 Orders) were identified, the majority of which were associated with fresh guano deposits. Over the past 40 years, 74 caves in Jamaica have been systematically surveyed for invertebrate diversity. Windsor Great Cave ranks in the top 10% for invertebrate species richness; all caves in this upper percentile support large bat colonies.

As increasing numbers of caves in Cockpit Country and across Jamaica are surveyed for their biological and physical diversity, the uniqueness and importance of Windsor Great Cave continues to be recognized and cannot be underemphasized. Because of its large size and diverse microhabitats, it supports one of the richest assemblages of cave-dependent fauna found anywhere on the island. The species found within Windsor Great Cave represent globally unique species, found nowhere else in the world. These species provide important ecological services that maintain the Cockpit Country ecosystem. The speed with which humans can destroy a cave system, particularly through intensive guano extraction and ecotourism, requires that careful monitoring and management of visitors to Windsor Great Cave be continued to prevent any further degradation to the cave and to allow the fauna to maintain their natural interactions.