While many countries have developed and expanded efforts to sustain and enhance the protection of biodiversity, the effectiveness of such programs, as well as the manner in which funds are distributed, has been questioned. We examined funding allocation decisions for species conservation in Spain at different governmental scales. Several factors that may impact conservation spending patterns and policy decisions were examined, including available scientific data, current scientific policies, and public awareness and perceptions of conservation needs. Our analyses revealed a strong connection between existing conservation policies and scientific information, research priorities and public concern. We found that there is a substantial bias in the taxa that are studied, the funding levels for those studies and public policy which triggers and supports the studies. The relationships, however, are not strictly cause and effect, but are instead enmeshed in a complex feed-back system in which conventional scientific activity acts as the main driver but is itself influenced by both policy and public perception. By acknowledging both the essential role of science in this system and the critical factors that can influence the acquisition of scientific information, a constructive dialog can be established that will propel conservation activities to a more productive and environmentally sound outcome.